Wonder Woman is from a culture where heroes are expected to kill their enemies since it was before wide-scale, long-term prisons were invented. It was not considered wrong or any shame in it. As a warrior trained to kill her enemy on the field of battle if necessary she will kill.

Some of Superman's foes are so powerful that the Phantom Zone is probable the only prison that can truly secure them. Superman vs The Elite raised a good point that after the Atomic Skull has escaped for the 5th time and gone on a killing rampage killing him is more pragmatic and maybe more heroic than locking him up until he escapes in about a week.

Superman himself is more of a protector and peacekeeper and not a warrior. So his way makes sense for him.

Of course, the modern age is different and killing should not be the most immediate option. If you have prisons that can curlycue hold them then by all means they should be imprisoned.