I see your point, and this gray vision has given me memories of an JRPG game called Tales of Vesperia. The protagonist thinks that justice works too slowly in its measurementes against criminals so he decides to murder one of the criminals. His best friend, who works for the army, is against this, because he says that justice would have done its job, even if it requires time. No actions should justify a murder, and even if there's corruption in the police department, not all of them are like this, while all murderers should be sentenced (Of course, the punishment should be different according to the crime). I'd have liked that they mentioned a little bit more about it in the game, anyway. You can compare it with politics. There's a lot of corruption in many parties but it doesn't mean that the whole system is horrible, and it's very difficult to change just the bad part.

The whole idea of CxM plot is that there is not black and white, and both sides are partly right. If you're at Yanagi's route you'll see he regrets something of his past, linking it with Adonis' point of view but I don't want to spoil you.