I respectfully disagree. I, personally, had no problem with the conclusion of the fight between Superman and General Zod in "Man of Steel":
1. It makes sense in terms of Superman being young and inexperienced in the film, therefore jumping to murder as a solution before thinking of any other non-lethal option on the spot - with the clock ticking down rapidly, mind you.
2. It works by making the world more realistic in tone, which was the intent with the DC Cinematic Universe in the first place.
3. It works by giving a solid and definitive reasoning behind this Superman's no-kill policy (a famous trope associated with the character) going forward, something that was weakly examined beforehand in other incarnations.
Here, in the situation provided at the end of the film, Superman reluctantly murdering Zod functions as a solution that kills two birds with one stone: Unlike the traditional depictions of the character where he refuses to kill straight from the beginning, based soley on the values of Jonathan and Martha Kent, we have a Superman in Cavill's take where it's still his parents' values that work as the reasoning for him to never kill, just this time it's to never kill AGAIN. Their lessons about mortality and responsibility are more powerful when examined this way because it's not one that was only taught, but was also LEARNED by the Man of Steel himself once crossing an unfortunate line that his parents had warned him about for a very long time. And with that said: He'll probably never cross it again in the world that is the DC Cinematic Universe. Job well done by Snyder and Goyer, if you ask me.