Look, I'm all for the idea of "Superman doesn't kill" but still there's times when it's called for. And, again, it was a case of what else was there to be done? Say he COULD stop Zod from killing the family and subdue him. Then what? Zod himself said he would not stop until all the humans were gone and Superman (as far as he, and we, know) had nothing else to do with Zod. And, again, he showed REMORSE over it. He broke down and WEPT. It wasn't something he wanted to do or something he liked doing.
I'll take that over Batman's "Well, I won't kill you. But I won't save you, either!" deal to Ra's in "Batman Begins."