If you don't want to see the hero finally killing off the villian to keep him from escaping yet again, don't let the villian escape.
If you don't want to see the hero using lethal force because nobody stays dead, so Red Skull is coming right back, then let the villian stay dead.
Eventually, Batclone's going to snap, and put EvilClown in the ground permanently, because OldArkham's a sieve and can't keep anyone inside and, hey hell, EvilClown's coming back anyways.
The choice you as GM make forces the choice that the players make.
Discuss things with your players, and, stick with it. Let the villain go to jail, or die, and stay there. Come up with a new villian, and move on.
Like Hermit says, it's about the genre you run (except I'd put self destructive villains in more Golden Age, but that's a quibble).
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A hero might or might not kill, depending on the circumstances. He might have to kill to save a life, he might kill accidentally, but he doesn't kill for no reason, or with no forethough.
A knight would kill, a policeman would kill, but they aren't casual killers.
Killing is an option, but not the preferred method of dealing with any and all situations.
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D
Nathan, after rolling his 6th consecutive 15+, crosses out the name on his character sheet, "I'm now Chris, the Gestalt of Incompetence."
Chris, sitting next to him, "Grrr."
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