You seem to be suggesting that not only is it morally acceptable for a superhero to take a life, but it is actually immoral not to do so.
Personally, I’d rather not see Spider-Man--or other superheroes--killing their villains if it goes against their established character and values. But I do not think that it would always be wrong or immoral for some heroes to kill. The scenario presented at the end of Man of Steel comes to mind, though I think the writers intentionally wrote themselves a situation where Superman would have no choice but to kill.
But I would respectfully disagree with your assertion that it is immoral for the hero to choose not to take a life. I think the suggestion that people have some kind of obligation to put the needs of society above the dictates of their own conscience is particularly troublesome. To repeat an earlier example, I would find it hard to find fault in someone who was asked by the government to drop a nuclear bomb during war and decided against it. I think it is important in a healthy society to respect one another’s belief systems, even if they are different from our own.
As I said earlier in the thread, heroes don’t leave their consciences at the door when they decide to fight crime. They’re risking their lives to protect people because they choose to, not because they are under any obligation to do so, aside from their own sense of responsibility.
Also, instead of blaming Spider-Man or Batman for what happens when villains escape, wouldn’t it be more appropriate to blame the government for not enforcing the death penalty?