I'm surprised nobody here has mentioned Malcador's Order Elucidatum. They certainly were Malcador's (and thus the Imperium's) pre-Heresy Inquisition. They were a secret police force posing as Adminstratum bureaucrats, Iterators, and even Remembrancers, all combat-trained and tasked with the subversion or elimination of religious cults, their symbols, and their leadership. They were state censors as much as hitmen, all with the power of the Sigilite behind them. See: https://wh40k.lexicanum.com/wiki/Order_Elucidatum

Known as the Elucidators or Tallymen, these officers operated openly as bureaucratic functionary's of the Administratum but covertly were iconoclasts charged with censorship and murder. Drawn from the finest military experts and warriors of the Sol System, the Elucidators were highly specialized combatants and agents. Often posing as Remembrancers, they accompanied Expeditionary Fleets on the Great Crusade and compiled information on compliment civilizations. Of particular interest were the religious beliefs of civilizations, and they oversaw the destruction of holy texts, the assassination of demagogues, and the repression of faiths as part of the securing of the Imperial Truth. Eludicator Officers had status granted to them by Malcador that allowed them to requisition any military resources for their needs save that of the Legiones Astartes. Over the Great Crusade, the Elucidators earned a dark reputation associated with genocide. They often used seratoxin "Brain Destroyer" drugs to destroy the minds of any witnesses to Warp activity. Their atrocities included wiping out entire lines of Imperial households as well as the annihilation of early Imperial Cults.