By the end of the movie the only thing really against Nick would be negative public opinion and I'd rather deal with that than have to be with a sociopath for the foreseeable future.
Because she got herself pregnant with his semen from the fertility clinic. He didn't want Amy to raise his child without him in his/her life. He wants to protect his child from Amy as much as he can, and he wants to prove to himself he can be the father that Bill Dunne never was.
Before I read you, I rewatched the end to understand how on earth she got pregnant. English is not my mother tongue and I seem to have missed some subtlety in the dialogue. Where is it alluded to the fertility clinic thing?