At some point, Villains need to die. If a state had the death penalty, I'm sure heroes might be tasked to take execution orders to the villains that can't be caught and held by regular means.
I mean, when you have multiple capital crimes committed by a villain, and convicted, and the only thing holding the law back from executing them is their ability to escape normal law enforcement, heroes need to step in.
It would be like normal people serving papers, except that the heroes would go grab the villains and forcefully bring them back. Since they probably have already been convicted of crimes in the past and should have already been executed, take them straight to the chair, and under hero guard, flip the switch.
This ideology of heroes never hurting anyone, even convicted mass murders, is a school boy fantasy. Even in comic books its unrealistic and only works if the story is forced by the writers. And it still doesn't sit well.This also applies to the trope 'If you kill me, you'll be just as evil as I am.' No they won't. Any hero that falls into this moral dilemma should be shot and hand off their abilities to someone with a pair. The only way I can see this as interesting story telling, is when this mindset is actually a known hindrance to the hero and his life, like Peter Parker in the early 2000's (haven't read Spiderman since they made 40 of them.)