The evil white colonizer BS is a severely overrated liberal myth. Mostly likely created by America-hating, communist sympathizer professors.
The first anti-colonial writer of note was the Dominican Friar Bartolome De Las Casas.
https://en.m.wikipedia.org/wiki/Bartolom%C3%A9_de_las_Casas
He was very influential, and his complaints were heard at the Spanish court. This led to a centuries-long policy of benevolence towards the natives by the crown, which persisted through changes of reign and dynasty. For three hundred years natives could always find a sympathetic ear at court.
And in the Church for that matter. There was a marked pro-native bias in the Spanish church.
Unfortunately royal/imperial policy was of limited effectiveness on the ground, the King was far away but the alguacil was right here. And contrary to popular misconceptions, the church was weak in the Spanish colonies. Too few priests and churches for the territory and population was the common story.