I'm with you on this one. Superman doesn't WANT to kill. He wont kill casually. Within a certain context he'll put himself in great LIFE THREATENING DANGER to avoid having to kill or cause undue harm to anyone, even an enemy.Yes. Superman kills Zod. Just like Superman killed Zod in Superman II. Just like Superman killed Zod in the comic book. Superman kills Zod. It's part of the story. The difference is that in Superman II, Superman happily kills a Zod who has been depowered and is not a threat, while in MoS, Superman reluctantly kills Zod to save a family and who will always be an existential threat to Earth.
But when the threat is too great and life will be threatened on an immense scale? He wont WANT TO do it. He might even have a mental / emotional breakdown afterwards because it's not in his nature to. But Kal will do the long term calculations of the safety of millions vs his moral code and if the math doesn't work?
HE WILL TAKE OUT THAT THREAT.
See SUPERMAN #22 (John Byrne's run)
That's why I had no problem with his decision at the end of MOS. As long as the ramifications of that action is touched on in later films I'm fine with it. The fact that to his knowledge that Zod was literally the only other Kryptonian left and that he was forced to kill him would affect ANYONE other than the coldest sociopath.