New France (17th - 18th century): the "no Black Robes - no fur trade" policy with the natives
16th - 18th century Europe: assimilation and/or killing of Anabaptists and others who did not conform to established religions
Canadian Residential Schools (also includes Anglican, Lutheran and others): the longest running genocide in world history. From fairly early on in New France, to as recent as 1996
And more...