...yet at the same time ignore that there is no "realistic" way that Superman could have stopped Zod without killing him...
That's an opinion, not a physically demonstrable fact. Just because the bad guy said killing was the only way, that doesn't mean we or the hero are required to believe him. What kind of superhero story ends with the hero surrendering to the villain's worldview? That's getting it backward. Villains are always trying to impose their cynical, violence-justifying narratives onto events, insisting that their way is the only way, but heroes generally reject those narratives and demonstrate the power of their own, more positive narratives. (Imagine if Return of the Jedi had ended with Luke deciding that Palpatine was right and he should just kill Vader.) Regardless of the morality of killing, Superman letting Zod's worldview win out is a failure for Superman as a character. Which is a pretty crappy way to end his debut story.
See, the problem with the whole "the character had no choice because of the circumstances" argument is that the characters and their circumstances don't exist. They're created by the writers, and the writers absolutely have the choice to make things happen differently. So I'm not criticizing the choice of an imaginary Kryptonian orphan. I'm criticizing the choice of David Goyer and Zack Snyder to construct the story in a way that would force Superman to kill. They didn't have to do that. They had the freedom to end the story in any number of different ways, and they chose to go with that one. And I have every right to disagree with that creative choice. Just as I have the right to disagree with their choice to create a climax that would destroy most of Metropolis for no story-relevant reason whatsoever and leave Superman helpless to prevent it.
So no, there is no contradiction there. In both cases, it's a disagreement with the creative choices of Messrs. Goyer and Snyder, their desire to do a gritty, cynical disaster-porn story that deconstructed Superman rather than a story that embraced and celebrated what Superman represents.