A choice that is inevitable is an absence of choice. It's also a product of the writing, which I found poor. A lack of follow up on the trauma of taking a life was disappointing, and though it looks to be addressed in bvs, that doesn't erase the disappointment I had with MoS.
There's also the fact that the scene in question poorly conveyed an impossible decision. You can argue he has no choice but to put Zod down for good, but in that specific scene, there were plenty of ways to save that particular family without snapping his neck.
True, but what then? Continue the fight and risk even more lives? It's not like Superman had anywhere to put him that could contain him. It also wasn't just about that particular family. Zod outright said his sole mission at that point was to kill everybody. Even if Superman attempted to take the fight elsewhere, without killing him, Zod would just continue trying to kill more people. Superman even attempting to save lives leaves Zod open to kill other people. Zod is a trained soldier. The longer the fight goes on the more accustom to his powers he gets which would likely result in Superman's death and the extinction of the human race.