While appearing on the Nerdist Podcast, Man of Steel screenwriter David S. Goyer defended the choice made by the title character during his climactic battle with General Zod. According to Screen Rant's transcript of the exchange, Goyer said it was "what's right for the story." He continued:
That exists entirely separately from what fans should or shouldn't think of that character. You have to do what's right for the story. In that instance, this was a Superman who had only been Superman for like, a week. He wasn't Superman as we think of him in the DC Comics…or even in a world that conceived of Superman existing. He'd only flown for the first time a few days before that. He'd never fought anyone that had super powers before. And so he's going up against a guy who's not only super-powered, but has been training since birth to use those super powers, who exists as a superhuman killing machine, who has stated, 'I will never stop until I destroy all of humanity.' If you take Superman out of it, what's the right way to tell that story? I think the right way to tell that story is if you take this powered alien who says, 'You can have your race back, but you have to kill your adopted race,' the moral, horrible situation to be in is to actually be forced to kill, not wanting to, the only other person from your race. Take Superman aside, I think that's the right way to tell that story.
The choice may make sense in that context, but it certainly was difficult for some to see a character wearing the El family crest snap another man's neck. Of course, a Superman who is willing to kill is a sharper contrast to a Batman who will not. If that comes into play in Batman v Superman: Dawn of Justice remains to be be seen.