The closest I can think of is the minion who works with the evil person cause they think that the end justifies the means.

Most immediately comes to mind is the story of WA4, where the minion is an elite military team whose goal is essentially good--the restoration of a wartorn world and the setting up of a democratic government--while the leaders are evil who want to restore the world through the use of an artificially evolved lifeform, which makes them make the military team resort to kidnapping, etc. etc. The lifeform's brother is even part of the military team, and he believes this is a way for him to protect and save his sister (and not in a twisted, evil sense).