How can one deal with a friend's situation when they are suffering from an internal conflict between honoring their father and hating him, after discovering a bad deed their father committed, which led to their alienation and feeling of revulsion towards him?

If the father has committed a reprehensible act, he thereby incurs sin. There is no blame upon the son for disliking in his heart what his father has done, for there is no accountability for heartfelt dislike. The son must denounce the reprehensible act he witnesses from his father with gentleness and respect, and he must be careful not to harm his father in any way, as that is an act of disobedience (to parents). He must accompany his father with kindness, even if he is a disbeliever. It is forbidden for the son to supplicate against his father for death or destruction, or to disavow his lineage, for all of that is forbidden disobedience. The son has done well by supplicating for his father with goodness and righteousness, and he must remain steadfast in that and offer advice to his father with wisdom and good counsel.