This can easy be put right, as far as the OP can do anyway. "He can say dad, I am sorry I got mad and insulted you, and I'd like to have a relationship with you , outside of your religion if you can manage that." The OP is a grown man. He has a wife now and this relationship is far more important to him at the moment. What does she think? Is she atheist too? It sounds like they were forced into marriage. Can they make it work, do they love each other? This is the important thing the OP has to concentrate on.
It's not immoral to eat meat, abort a fetus or love someone of the same sex...I think that about covers it
