Well, I feel like if it had been executed a bit better, it could have been a really powerful moment that would have elevated the film. The movie ends in a bittersweet way. Superman saves the day, but to do so he's forced to go to a dark place and do a bad thing. You've got a hero who was victorious, but that victory did not come without sacrifice. You've got Superman's vow of pseudo-pacifism and reverence for life now reinforced by an element of guilt and shame. You could raise the notion in people's minds that an act can both be unquestionably and completely wrong and immoral and also be unavoidable and necessary. You can cement the notion that these are the kinds of ethical decisions that he has to make now that he's put on the cape. He can't just keep to himself and occasionally save people from fires anymore, he has to navigate the complexities of the world on a massive scale where the outcomes of his decisions mean life or death.
The killing of Zod, if handled well, could have been a pretty great and harrowing way of ending a film that both deconstructs and venerates Superman's classical boy scout morality in a very visceral and human way.
But it wasn't handled well so I say cut it.