I had no idea there was a deleted scene where we see the villains alive until this thread. I haven't seen the movie in many years, and my immediate takeaway was always that Superman crushed Zod's hand, flung him against the wall, and down the pit to his death, all with no remorse or attempt to bring him in alive.
You can go "Well, actually" all you like, but the fact remains that in the scene Superman is facing someone who is now not a threat to anyone and at the very least breaks many of his bones all without any need. I have many issues with MoS, but I find the neck snap to be more justifiable than how Superman II handled it.