If money was given to a person for a certain purpose, then he does not have the right to spend it on anything else, or to give some of it to anyone, except with the permission of those who gave it to him. Additionally, he must return whatever is left over of it, if there is anything left over.

1- If your father’s aim was to achieve a specific purpose, then you do not have the right to spend the money on anything else, even if he did not emphasise that it was a trust and was only to be used for that purpose. 2- But if he was only advising you [as to how to spend it] and he would not mind if you spend it on something else, then there is no blame on you in that case.

There is nothing wrong with you making use of this scholarship, even if the organisation commits some haraam actions, or some of its sources of income are from haraam wealth, because in the case of money that is haraam because of the manner in which it was earned, it is haraam only for the one who earned it, and it is not haraam for the one who takes it from him in a permissible manner, such as if it is a gift or reward and the like. With regard to your father’s participation in this organisation, that is subject to further details, which may be seen in the long answer.