Am I obligated to repay the scholarship amount to my father, knowing that the money will go to my father and not to the merchant who granted it?

You are not obligated to repay your father the value of the grant, as it was a gift from the merchant to you, which you received and disposed of. The fact that you obtained it because your father works for the merchant does not obligate you to pay it to him if he requests it. However, you are obligated to honor and be kind to your father. If he is in need of financial support and you are affluent, then you are obligated to provide for him. Ibn Qudamah said: "A man is compelled to spend on his parents and his children, both males and females, if they are poor and he has the means to spend on them."