Again, you're attributing the actions of invaders - in this case, Spanish - to their religion.
Sure, they planted a flag with a cross on it right next to the Spanish one, but their excuse - also used by other European colonizers throughout the Americas and the World - that raping, stealing, murdering, enslaving indigenous populations and Africans brought here was justified because those were heathens ran thin after those people converted to Christianity and adopted the dress and customs of colonists.
Nevertheless, there were missionairies that had also given safe refuge to them in places throughout the Southwest, Mexico, the Amazon, etc. CATHOLIC missionaries.
Not saying they all did or that some weren't abusive, but some was better than none, which is what we got from others, including the US Gov't after signing treaties with them only the massacre them anyways.