So let’s talk about the basic assumption of “comic book hero”. In Marvel/DC, many “heroes” have tacit or explicit local or federal mandate to allow them to function. The Avengers were legally empowered in various times/continuities, as has Superman, as have others.
Some skirt this by being subject to weird varieties of ambassadors of nations that don’t agree to prosecute (as do some villains!).
So it boils down to what rights has the supporting government given me, and is the target been designated as a “wanted dead or alive” - such as using an IRL example, Osama bin Laden.
Because if the i’s are dotted, and the t’s are crossed, I absolutely would kill Joker and the Red Skull based on their actions to date (using two of your examples). Sure, it might cut into my merchandising profits if parents find me too brutal and won’t buy the kids my action figures, but it’s worth it in those two examples.
But even if I have the right to kill them in the course of duty, I’m not going to kill mooks and the like, because the system should be able to deal with them, and I don’t want to be seen as a heartless killer (see merchandising again!).
If I’m in a world where I’m an out and out vigilante, hunted by the police as much as the rest of the criminals are, then I’ll kill those I hold responsible (again, bosses and lieutenants, not so much mooks) if I can -get away with it-. Make it look like an inter-gang level conflict, or inter-group fighting. I want the cops/feds to think that while I’m a criminal, they’d rather let me take out other criminals, and stay under the radar.