This is where I have a fundamental problem. As a piece of English, "This action is Evil but is nevertheless morally correct" is contradictory in nearly all cases.
Are you saying that every judge or jury which has imposed the death penalty, and every person in the justice system who had a part in carrying it out believes taking a life to be morally correct? How about every soldier or police officer who has ever fired a weapon? I suggest, rather, that they are taking an action which, in isolation, is not morally correct ("Thou shalt not kill") in a context in which it is considered morally correct (defense or protection of the innocent, for example).
If, in fact, for whatever reason, it is morally permissible to kill the prisoner, then doing so is per se not evil. If it is morally obligatory to do so, then doing so is good. That's what the words "good" and "evil" mean!
Now we are getting to specific contexts. And here we can have one character who considers the risk to the innocent is outweighed by the right of the prisoner to live, and another who considers the opposite is true. Both making their decisions based on Good reasons, and weighing the various aspects of Good to come to a conclusion. It doesn't make either, or both, "evil", or "non-good" because they must choose a compromise when all ideals of Good cannot simultaneously be met.