Under the Doctrine of Discovery , Spain and Portugal saw the Catholic Church as giving leave to subjugate, enslave, and torture indigenous peoples in the name of bringing them into the faith. While many Europeans would look to this doctrine to rationalize Aboriginal conquests, the Spanish were the most brutal.
At the same time, French emphasis on proselytizing over permanent settlement in what is now Canada, is credited by many historians, along with the fishing and fur trades, for maintaining a more equal Aboriginal/European realationship for a much longer period than in the rest of the Americas.
The boarding school experience in the US and Canada destroyed individuals and whole cultures. Religious reformers were also responsible for many failed assimilation attempt. Yet, today, religious schools often provide the best education on reservations.
For more on this topic, see Aboriginal Rights, The Church by Tyson Yunkaporta.