I think the "excuse" to why it was morally sound for Superman to kill them was because they were regarded monsters or in-human. There fore it's not inhuman to kill them if they were not human to begin with.
Doomsday, for example, he was more of a biological weapon monster than a living being.
Okay for Doomsday and "evil" MXYZPTLK but not with the others. By that logic than Superman is also in-human since he came from the same place as Zod.
Also not as dramatic as movie version, but in comic version Superman also killed Zod, Quex-Ul, and Zalor by using a combination of gold and green Kryptonite.
Pink-clothed version?
The one with bouncy heart shaped, the original costume.