Biggest Catholic Church in Canada at that time was from British controlled Ireland. Catholic emancipation of 1829 legalized Catholicism in Ireland, however Brits had influence over the church and handed the previously independant church, who organized risings and rebellions against them, to Rome. The Papal states were pretty well puppets of the monarchs of empire since the 1300s. Annexed by France and released by Coalition against Napolean in 1814, if I remember the year correctly of the top of my head. The Roman Catholic church in Ireland then imposed the Inquisition which had not been in Ireland up til then, and used it as a tool to stop further Rebellion. Roman Catholic Church was a effectively a puppet used to achieve their aims. Inquisition was first imposed by the French government to prevent heresy within the church in newly conquered territory. Papal States were annexed in the wake of the rise of Italian Nationalism around 1870s or something like that. The Vatican was released by Mussolini in 1929. Pope didnt even have full control of the papal states themselves, highly unlikely they were really running stuff in the colonies. Missionaries also helped teach the Natives European agricultural practices to sustain themselves in the wake of the destruction of their way of life due to colonial settlers converting their hunting grounds to farmland.

Edit: Also after the Catholic emancipation they started to actually enforce the Penal laws. They had not had much success because the Catholics in Ireland stirred stuff up if they did. Thus in my family, my Nana’s father was Irish and Protestant and her mother was a British Catholic. The men in the family were protestant and their wives were Catholic so the men could own land.