Bear in mind this is the same Superman who gave up his powers and responsibilities to bed Lois, then when that didn't work out so great he super rufied her and then went back to the diner to assault and humiliate the bully out of petty revenge. He's already compromising his values for movie audiences.
Now did the villains die at the end? In both the Lester version and the Donner version based on the narrative provided we see Superman kneel before Zod then he crushes every bone in his hand before throwing him across the room. Zod then falls into the foggy abyss, as does Non when he tries to fly. Lois gets payback by punching out Ursa who also falls, her voice trailing off in the distance without ever hitting the bottom. I just showed this sequence to my 6 year old son and I asked him what happened. He told me they fell in a deep hole and when I asked him what he thought happened to them at the bottom, he closed his eyes, stuck his tongue out the side of his mouth and said "uuuggghhh." Just to be sure I asked him to verbalize his opinion and he thinks they died.
In both versions, there are no UN police there to escort the prisoners off to jail, that only occurred in a deleted scene. Donner and Lester both intended for the villains to die for their crimes against humanity because movie audiences demand those consequences against enemy combatants who invade, decimate and conquer the United States of America. Donner is only slightly more "authentic" in his portrayal of Superman by having him spin around the earth to turn back time which 'un-kills' the villains and restores them to the phantom zone.
So Lester had Superman kill and Donner had Superman un-kill after the fact but killing was done in both cases. Some fans experienced cognitive dissonance over this act and so they project alternative scenarios onto the narrative to resolve the contradiction in their minds but that doesn't alter the past events as depicted by either filmmaker.
After all, it is forbidden to interfere with human history, or to embrace deleted scenes as canon.