The Church in Tsukihime is portrayed this way. They can't go too overboard because they're supposed to be secret. The only reason they're not trying to kill Arcueid is because, well, she's essentially unkillable. They gave up. Supplementary materials indicate that they prefer the 'kill the evil non-human, burn the body, and cover up all the evidence' course of action, and ask questions only if they are unable to actually kill said non-human, as in the case with Arcueid, Ciel, or Wallachia.
Damon Gant of the first game puts the extrem(e) in Well-Intentioned Extremist. Among his acts are murdering a co-worker to get a criminal, Joe Darke, convicted of murder, the manipulation of the crime scene to make it look like an innocent girl had done the deed by accident in order to make her older sister Lana into his pawn, the murder of ANOTHER co-worker who wanted to investigate the previous murder two years later, the coercion of Lana to take the fall for THAT murder, generally making Case 1-5 a hell for Mr. Wright and much more. His reasons for doing all this was to gain total control over the police force, so that criminals who were obviously guilty (such as Darke had been) would be brought to justice, no matter what.
Edgeworth in the first game appears at first to be an Amoral Attorney who prosecutes innocent people for the sake of his own record. However, it is eventually revealed that he honestly believed in the guilt of all the people he used illegitimate methods to try to sentence, making him this.
Phoenix Wright Ace Attorney Dual Destinies has many of the students of Themis Legal Academy, aka an entire law school become convinced that this path is the best one. This is thanks to the efforts of the defense attorney teacher, Professor Aristotle "The Ends Justifies The" Means. He makes a point to lecture students and protagonists alike that they're in "The Dark Age of The Law" where all lawyers are in danger of dooming their clients or letting criminals roam free if they don't employ his practices. Believe it or not, he's actually pretty friendly, his cynicism aside. He's also a murderer, accepts bribes from students, finds insulting his ideology worse than accusing him of murder, and not a pleasant man one bit.