The full cut shows Superman turning over all three phantom zone criminals to police custody after the events in the fortress. This was even broadcast on the ABC television version in the '80's.
TV cuts are padded to fit timeslots. The official release of the movie does not show the Kryptonian Criminals getting arrested. (IIRC, doesn't this scene also show the FoS being destroyed which is still present in the other Superman movies?)
We didn't see Zod's broken body in a pool of blood either. We don't know how fall those pits go. They probably hit the ground sometime after being thrown and ended up being injured though.
FOS was only in the first two movies, not in the third or fourth. I'll treat Superman Returns as its own thing since they had completely new writers/producers/actors.