He is confused about the meaning of this verse

May Allaah help us and you to do that which He loves and which pleases Him. The difference between the guidance and true religion that Allaah has revealed in His Book and what the Christians say about the Prophet of Allaah ‘Eesa (Jesus – peace be upon him) is the difference between faith and disbelief (kufr), between Tawheed and shirk, between guidance and misguidance. It is the difference between darkness and light. We ask Allaah to illuminate our hearts with Tawheed and faith in Him alone. 

It should be noted that if a person is confused about the meaning of any ambiguous passage [al-mutashaabuh] in the Book of Allaah, he must understand it in the light of the definitive passages [[al-muhkamaat], which form the majority of this clear Book. That is the source to which reference should be made in order to understand it, know its rulings and learn its lessons. He should not counter one verse with another, or look for contradictions in the revelation, or look for the ambiguous passages which may cause confusion to him or to other people, ignoring the clear and definitive passages. That is the way of the people of innovation and is misguidance, may Allaah keep us and you safe and sound. Allaah says (interpretation of the meaning): 

“It is He Who has sent down to you (Muhammad) the Book (this Qur’aan). In it are Verses that are entirely clear, they are the foundations of the Book [and those are the Verses of Al-Ahkaam (commandments), Al-Faraa’id (obligatory duties) and Al-Hudood (laws for the punishment of thieves, adulterers)]; and others not entirely clear. So as for those in whose hearts there is a deviation (from the truth) they follow that which is not entirely clear thereof, seeking Al-Fitnah (polytheism and trials), and seeking for its hidden meanings, but none knows its hidden meanings save Allaah. And those who are firmly grounded in knowledge say: “We believe in it; the whole of it (clear and unclear Verses) are from our Lord.” And none receive admonition except men of understanding”

[Aal ‘Imraan 3:7]

The verse which you quoted does not support the Christian view in any way whatsoever, rather this verse, when taken in context, refutes the Christians and clearly demonstrates their misguidance and their disbelief in the Lord of the Worlds.  

Allaah says (interpretation of the meaning): 

“This is a part of the news of the Ghayb (Unseen, i.e. the news of the past nations of which you have no knowledge) which We reveal to you (O Muhammad). You were not with them, when they cast lots with their pens as to which of them should be charged with the care of Maryam (Mary); nor were you with them when they disputed.

45. (Remember) when the angels said: ‘O Maryam (Mary)! Verily, Allaah gives you the glad tidings of a Word [“Be!” — and he was! i.e. ‘Eesa (Jesus) the son of Maryam (Mary)] from Him, his name will be the Messiah ‘Eesa (Jesus), the son of Maryam (Mary), held in honour in this world and in the Hereafter, and will be one of those who are near to Allaah.

46. He will speak to the people, in the cradle and in manhood, and he will be one of the righteous.’

47. She said: ‘O my Lord! How shall I have a son when no man has touched me?’ He said: ‘So (it will be) for Allaah creates what He wills. When He has decreed something, He says to it only: “Be!” — and it is.

48. And He (Allaah) will teach him [‘Eesa (Jesus)] the Book and Al-Hikmah (i.e. the Sunnah, the faultless speech of the Prophets, wisdom), (and) the Tawraat (Torah) and the Injeel (Gospel).

49. And will make him [‘Eesa (Jesus)] a Messenger to the Children of Israel (saying): “I have come to you with a sign from your Lord, that I design for you out of clay, a figure like that of a bird, and breathe into it, and it becomes a bird by Allaah’s Leave; and I heal him who was born blind, and the leper, and I bring the dead to life by Allaah’s Leave. And I inform you of what you eat, and what you store in your houses. Surely, therein is a sign for you, if you believe.

50. And I have come confirming that which was before me of the Tawraat (Torah), and to make lawful to you part of what was forbidden to you, and I have come to you with a proof from your Lord. So fear Allaah and obey me.

51. Truly, Allaah is my Lord and your Lord, so worship Him (Alone). This is the Straight Path”

[Aal ‘Imraan 3:44-51] 

Shaykh al-Islam Ibn Taymiah (may Allaah have mercy on him) said:

This demonstrates in several ways that he was a created being and was not as the Christians say.  

For example, it clearly means that he was a created being, as it says, “So (it will be) for Allaah creates what He wills. When He has decreed something, He says to it only: “Be!” —and it is”. As Allaah says elsewhere (interpretation of the meaning): 

“Verily, the likeness of ‘Eesa (Jesus) before Allaah is the likeness of Adam. He created him from dust, then (He) said to him: “Be!” — and he was”[Aal ‘Imraan 3:59]

And Allaah says in Soorat Maryam (interpretation of the meaning): 

“Such is ‘Eesa (Jesus), son of Maryam (Mary). (It is) a statement of truth, about which they doubt (or dispute).

It befits not (the Majesty of) Allaah that He should beget a son [this refers to the slander of Christians against Allaah, by saying that ‘Eesa (Jesus) is the son of Allaah]. Glorified (and Exalted) be He (above all that they associate with Him). When He decrees a thing, He only says to it: “Be!” and it is”

[Maryam 19:35] 

And he said: His name is the Messiah ‘Eesa ibn Maryam (Jesus son of Mary), so Allaah has told us that he is the son of Maryam, and that he is held in honour in this world and in the Hereafter, and will be one of those who are near to Allaah. All of these are attributes of created beings. 

Maryam said: “How shall I have a son…?” This shows that the Messiah, who is the Word, is the son of Maryam, not the son of Allaah, may He be glorified and exalted. 

Allaah says in Soorat al-Nisa’ (interpretation of the meaning): 

“O people of the Scripture (Christians)! Do not exceed the limits in your religion, nor say of Allaah aught but the truth. The Messiah ‘Eesa (Jesus), son of Maryam (Mary), was (no more than) a Messenger of Allaah and His Word, (“Be!” — and he was) which He bestowed on Maryam (Mary) and a spirit (Rooh) created by Him; so believe in Allaah and His Messengers. Say not: ‘Three (trinity)!’ Cease! (it is) better for you. For Allaah is (the only) One Ilaah (God), glory is to Him (Far Exalted is He) above having a son. To Him belongs all that is in the heavens and all that is in the earth. And Allaah is All‑Sufficient as a Disposer of affairs.

172. The Messiah will never be proud to reject to be a slave of Allaah, nor the angels who are the near (to Allaah). And whosoever rejects His worship and is proud, then He will gather them all together unto Himself.

173. So, as for those who believed (in the Oneness of Allaah — Islamic Monotheism) and did deeds of righteousness, He will give them their (due) rewards — and more out of His Bounty. But as for those who refused His worship and were proud, He will punish them with a painful torment. And they will not find for themselves besides Allaah any protector or helper”

[al-Nisa’ 4:171-173]

So Allaah forbids the Christians to exaggerate concerning their religion or to say things about Allaah that are not true, and He states that the Messiah ‘Eesa ibn Maryam is a Messenger of Allaah and His Word which He bestowed upon Maryam, and a spirit created by Him. He commands them to believe in Allaah and His Messengers, and tells them that he (‘Eesa) is His Messenger. He forbids them to say “Three” (i.e., trinity) and says: “Cease! (it is) better for you”. This is a rejection of their doctrine concerning the Messiah which says that “he is a true god from a true god, from the essence of his father.” 

Then He says: “glory is to Him (Far Exalted is He) above having a son” – declaring Himself to be far above having a son as the Christians say. Then He says: “To Him belongs all that is in the heavens and all that is in the earth”, telling us that all of that is His dominion, in which there is nothing of His essence.  

Then He says: “The Messiah will never be proud to reject to be a slave of Allaah, nor the angels who are the near (to Allaah)” i.e., they will never deny that they are slaves of Allaah, may He be blessed and exalted. After such a clear statement, can anyone think that what is meant by “His Word” is that he is a god and creator, or whatever such statements of kufr they make? 

Rather ‘Eesa alone is described as the Word because he was not created in the usual way in which others are created, rather he was created in an extraordinary way: he was created by the command of Allaah: “Be!” This is the Word in question; he was not created by means of a male fertilizing a female, as is the usual way in which Allaah creates human beings. 

The fact that ‘Eesa (peace be upon him) is a Word from Allaah and a spirit created by Him, as is indicated in the texts of the clear Revelation, does not mean that he is part of Allaah who emerged from Him and is connected to His essence: glorified and exalted be Allaah far about what the wrongdoers say. Rather what it means is that he came from Allaah, as Allaah says (interpretation of the meaning): 

“And has subjected to you all that is in the heavens and all that is in the earth; it is all as a favour and kindness from Him”

[al-Jaathiyah 45:13] 

“And whatever of blessings and good things you have, it is from Allaah”
[al-Nahl 16:53] 

“Whatever of good reaches you, is from Allaah, but whatever of evil befalls you, is from yourself”

[al-Nisa’ 4:79]

And Allaah says concerning our Prophet Muhammad (peace and blessings of Allaah be upon him) (interpretation of the meaning): 

“Those who disbelieve from among the people of the Scripture (Jews and Christians) and Al‑Mushrikoon, were not going to leave (their disbelief) until there came to them clear evidence.

2. A Messenger (Muhammad) from Allaah, reciting (the Qur’aan) purified pages [purified from Al‑Baatil (falsehood)]”

[al-Bayyinah 98:1-2]

These are all things that come from Allaah, and they are all created. 

The phrase “a spirit created by Him (or from Him)” is used only of the Messiah because he was breathed into his mother by al-Rooh (Jibreel – peace be upon), and she became pregnant with him from that breath. This is something other than his rooh (soul) that he shares in common with the rest of mankind. He is distinguished from them by the fact that his mother became pregnant with him from this breathing in of the spirit, hence he is called a spirit from Him. See Daqaa’iq al-Tafseer, 1/324 ff. 

Moreover these verses clearly state that Allaah created him, and that Allaah creates whatever He will; nothing is beyond Him in the heavens or on earth. And ‘Eesa himself (peace be upon him) said that the signs and miracles that he brought were from Allaah and happened by His leave, a sign to them of His Oneness. Then the verses conclude with a clear statement of what is meant here, which is the command to worship Allaah, the Lord of ‘Eesa and the Lord of those to whom ‘Eesa was sent. This clearly indicates that what the Christians say about ‘Eesa and his mother is false, and it plainly refutes their kufr and misguidance. 

This verse also tells us that ‘Eesa is a Word from Allaah, and it points to the meaning of that. This is narrated in the Sunnah of the Prophet (peace and blessings of Allaah be upon him). Al-Bukhaari (3435) and Muslim (28) narrated from ‘Ubaadah (may Allaah be pleased with him) that the Prophet (peace and blessings of Allaah be upon him) said: “Whoever bears witness that there is no god except Allaah alone, with no partner or associate, and that Muhammad is His slave and Messenger, and that ‘Eesa is the slave of Allaah and His Messenger, His Word that He bestowed upon Maryam and a spirit from Him, that Paradise is true and Hell is true, Allaah will admit him to Paradise depending on his deeds.” According to another version: “… that ‘Eesa is the slave of Allaah and the son of His female slave.” 

Al-Qurtubi (may Allaah have mercy on him) said: What this hadeeth aims at is to warn against what the Christians fell into of misguidance concerning ‘Eesa and his mother. 

Another scholar said: Mentioning ‘Eesa is a reference to the misguidance to the Christians, because their belief in trinity is pure shirk. The same applies to the use of the word “His slave”. Describing ‘Eesa as “His Messenger” is a reference to the misguidance of the Jews because they deny that He was a Messenger and they slandered him and likewise his mother, saying things of which they were innocent. 

The words “son of His female slave” are intended to honour him.