If a parent is intentionally harmful to his or her children, then I don't believe the commandment applies, although there are several opinions on the matter. It's a similar situation to a parent asking a child to violate Jewish law, which is something that shouldn't be done, even if a parent says so.
Yes indeed, but parents also are required to love their their children, provide for their needs and teach them the right way of life. Your father seems to be violating these rules, therefore he is not a Jew.