The obligation to honor ones parents is based on two separate concepts. There is the rational issue that one is obligated to express gratitude to anyone who performs a favor, and parents who raise a child are owed the ultimate debt of human gratitude. However, in this case the gratitude seems to be limited to having brought the child into this world but not actually raising him. Of course this in itself is no small matter, because if not for your father you would not exist today. Additionally, there is an obligation to honor ones parents because Hashem commanded us to, just like we must eat kosher etc. even if we don't understand the reasoning for the commandment. This would certainly be equally applicable in this unfortunate situation.
There is a discussion in the poskim if the obligation to honor one's parent applies to a Rasha, a parent who is wicked. Such a determination would of course require the evaluation of an objective person familiar with the details of the circumstances. In any event, the general consensus of the Poskim is that one must honor even a wicked parent, regarding this point moot.