A lot of so-called "purists" apparently had a huge problem with that because Superman (apparently) doesn't kill.
-Superman doesn't kill
-Zod should have been invulnerable (they sort of left us to glean that - Superman's been here his whole life, he's stronger and Zod's full invulnerability hadn't quite kicked in yet.)
However, I felt the movie conveyed the reluctance and remorse Superman felt. Mrs. Midnight did not like the ending, because "Superman doesn't kill."
Personally, I would have preferred putting Zod back in the Phantom Zone (which was Nolan's preference, as well, apparently). However, IF Superman is going to have to kill, MoS handled it about as well as possible.
This post was edited on 6/26 at 7:58 am