In the Donner cut you see them arrested and taken away, now without powers, presumably to a human military prison Which could be a lot worse if they went there to get experimented on Look at Tal Roh Morgan in the show and Sasha Supergirl in Flash film Lester did not use that bit Most people interpret them not being killed, they go down a slide to a dungeon then get put back in the Zone Even if you see this as Superman kills Zod, he didn't kill the other two Lois hit Ursa and the Doofus fell in himself Although ... Superman could have flown at super speed and saved them It's down to your interpretation