Sooner or later, Nick actually will kill Amy — for the good of his son.
Think about it. Even with Nick around to keep an eye Amy and make sure she can't pull any of her schemes again, any kid growing up around her will still be severely messed up. Of course, you could say the same for Nick, though he's obviously a better choice than Amy. Nick is also self-aware enough to realize he's not a good guy. So eventually, he decides the best thing for his son would to be the hell away from Amy and Nick. And the best way he can think of to accomplish that is to actually kill Amy, and go to jail for her murder. The kid goes to foster care, or perhaps to someone in Nick or Amy's family — either option would provide a far better chance of the kid actually having a happy life than he would've had with Nick and Amy as parents.- Perhaps the kid will end up with his Aunt Margo.
