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.
Also from Dual Destinies, we have Aura Blackquill. She's not the most pleasant person to talk to, and has an intense hatred for the legal system due to the conviction of her brother, Simon. However, she doesn't actually seem all that bad... until she takes several visitors to the Space Museum (including Phoenix's own adopted daughter) hostage, and begins threatening them in exchange for Athena Cykes, whom she believes to be the true culprit of the crime her brother was arrested for. All of this was to force a retrial, in hopes that her brother's sentence would be overturned. Especially since his execution was only a day away. Luckily, Phoenix is able to earn a happy ending for both Simon and Athena, and she turns herself in after everything is said and done.
Akane from the Zero Escape series (Nine Hours, Nine Persons, Nine Doors & Virtue's Last Reward) would be considered this from most people's viewpoints. Not really a "villain", yet not a woman of pure gold either, her intentions and goals in the games are for her to save her own life and save the world from a fatal viral infection in '999' and 'VLR' respectively. Good goals, in anyone's book. However her methods for achieving such goals include kidnapping people, placing bombs into them, forcing them to play deadly games, blowing some people up, and in several alternative histories indirectly having caused and not prevented things such as mass-murders, bombs blowing up groups of people, mass-suicides and people having been torn from their loved for decades. Considering that the game runs on the "many worlds theory", basically making every timeline you see something that technically happened to the respective versions of the characters, it means that she was technically responsible for many horrific things. Trying to save her own life, and the world, is all well and good but it's one thing to go to THOSE lengths to do so.
Zero II/Delta/Brother, the Big Bad of Zero Time Dilemma qualifies as well. In the timeline that leads to Virtue's Last Reward, he killed 6 billion people with Radical-6 to have a 75% chance of killing the "Religious Fanatic", who would otherwise wipe out humanity through nuclear war. He also forces the participants of the Dcom experiment to take part in his deadly "Decision Game" to ensure his own birth and to create a timeline where the Religious Fanatic will be stopped.