The Circles from the Deva Series. They firmly believe that artificial magery will lead to The End of the World as We Know It and seek to kill Hayate and friends for using Devices. Admittedly, there is a smidge of truth in their beliefs, but the extents to which they go, combined with their insistence on refusing Hayate's offers, do not help their case.
Subverted in the Sonic the Hedgehog and Sailor Moon crossover Chaos Infinity. Chessmaster/Mad Scientist Dr. Eggman manipulates the Sailor Scouts into thinking that Sonic and his friends are the ones responsible for the crisis in Tokyo and pushes them to fight each other, thinking that the Scouts are too much for his archenemies to handle. His plan fails when Sonic gathers enough Heroic Resolve to pull out his own Chaos Blast to overpower their rivals and calls out BOTH the Sailor Scouts and the people of Tokyo for their mistreatment. And then Eggman nearly kills Sailor Moon when using her and the Master Emerald as batteries for another one of his war machines to take out Sonic for good and everyone knew from then on who was really friend and foe. Again, it backfires. After stopping his final weapon, the Sailor Scouts and the Freedom Fighters become friends.
In the Pony POV Series, one of the Alternate Universes that Applejack sees at one point is a world were the Mane Cast have become a group of dictators who brainwash and otherwise brutally suppress anything "disharmonic". They are actually based off of the Justice Lords from the Justice League series.
Subverted in Cheerilee's Garden. Cheerilee justifies her many brutal murders by claiming that she's doing the world a favor by ridding it of degenerates and corrupting influences ("weeds"), but just in case the reader wasn't already tipped off by her obvious eagerness and pleasure in committing such acts, Twilight flat-out states in the third chapter that Cheerilee is nothing more than a HedonisticSerial Killer.
The Law Heroine in Goddess Reborn Chronicle, whose soul was bonded to an angel-until she finds herself better treated by enemies than allies, questioning her own faith and motivations.
In Touhou canon, Yukari Yakumo is usually portrayed as the overseer of Gensokyo, when working being a Trickster Mentor to Reimu and tending the Hakurei Border. However, when the fic oges Darker and Edgier, Yukari will usually be a ruthless knight templar, that measures no consequences in order to keep the barrier up and Gensokyo safe. This goes from hunting Rin, provoking a small war with Yuuka and nearly executing Remilia for her failure in Imperfect Metamorphosis or spiriting away selfish kids to destroy the balance of Gensokyo in order to keep the place busy and prolong its lifespan in Diamond In The Rough.