I think the problem is not about the hero or the villain, but the government and the justice system in the comic. If it could work like in real life, the villains would be thrown into jail and it would be over. But in the comic, they just keep coming out over and over again because of their popularity, this is the REAL problem.
If the justice system is not useful, keep the NO KILL code would be dumb. Such as we don't question Zorro or Robin Hood to have such code because there was no justice in their story background.