The birth of the Chantry took place more than nine ages ago; the mists of time have obscured once well-known facts. It is commonly believed the Chantry alone created the templars and the Circle of Magi. Few recall there was ever an Inquisition. Those who do, believe, it predated the Chantry, hunting cultists and mages in a reign of terror ending only upon its transformation into the Templar Order. This is not quite the truth.
One must keep in mind the state of Thedas prior to the Chantry's creation: a world where the only source of order - The Tevinter Imperium - had fallen apart. People blamed magic for the death of Andraste, the Blight, the terror they saw every day - and not without reason. Abominations and demons rampaged the countryside. No one was safe. Disparate groups of men and women initially formed the Seekers of Truth, determined to reestablish order because no one else would do what was necessary. The truth they sought, the question they tried to answer, was how to restore sanity in a world gone mad.
Was theirs a reign of terror? Perhaps. Evidence suggests they were as vigilant in their protection of mages as they were of regular people. When they intervened, they convened an ad hoc trial to determine the guilty party. This even application of justice led to their poor reputation; the Seekers came down against every group at one time or another, their "Inquisition" gaining notoriety for being on no one's side but their own. They considered themselves good people, however - followers of the Maker's true commandments. This was never more evident than when they lay down their banner in support of the fledgling Chantry. They believed with all their heart that the Templar Order was the answer a desperate Thedas needed in a terrible time. Ultimately, the Inquisition was composed of independent idealists, not Chantry zealots; that is the truth.
--From In Pursuit of Knowledge: The Travels of a Chantry Scholar, by Brother Genitivi