So, Superman, faced with the choice of humanity or killing literally the last Kryptonian left aside from himself, breaks Zod’s neck. It ticked off a lot of nerds, even though Superman has killed Zod before, and Goyer gets into detail on it. The big takeaway, though, is really this:
“Also our movie was in a way Superman Begins, he’s not really Superman until the end of the film. We wanted him to have had that experience of having taken a life and carry that through onto the next films. Because he’s Superman and because people idolise him he will have to hold himself to a higher standard.”
Goyer also points out that “Superman doesn’t kill” comes from the comics, and that viewers who didn’t grow up reading Superman might be a little confused as to why the genocidal maniac with superpowers was left alive. But that’s really the key point, there, that Superman doesn’t know the extent of himself.
Personally, one has to ask: Did Superman really have another option? The comics are getting into this, a bit, with Superman Unchained, but what’s he going to do? Keep Zod locked up in a magical prison we find in the third act? Have Ryan Reynolds show up and cart him off to Oa?
Either way, this is probably just fuel for the flames. But, if nothing else, at least Goyer has a good reason for it.