I highly recommend the book The Fourth Part of the World by Toby Lester. It is a fascinating account of the discovery of the New World, specifically the Americas, and the political and religious cultural dynamics at play both before, during, and after their discovery.

You may be interested in looking up Bartolome De Las Casas and his most notable work "A Short Account of the Destruction of the Indies". He was a Spaniard who immigrated with his father to the New World in 1502 when he was 18, to become landowners and participate in the conquests. His most notable work, mentioned above, is his firsthand account of the atrocities he witnessed and was a part of during his time as part of the conquests of Hispaniola and Cuba. It is a book that I think everyone should read in their lifetimes... if they can stomach it. It does have a habit of becoming unapologetically graphic, to the point where I've heard from several people in the class where we read this, that they could not get through it. Though I believe that was the point. It was written some decades later as a letter to Charles V (and later Phillip II) and to the Pope, as a way of persuading them to end the atrocities committed in the Americas.

He was so affected by the horrors he saw and brought on the natives that he became a priest (and later a Dominican friar) and spent the rest of his life trying to atone for his sins and advocating for the rights of the native tribes. Interestingly, he did become the first person to be ordained in the New World. He was not the first, Catholic within the church to argue that the natives were humans with souls and should be converted and treated equally, though his voice did become one of the loudest and most influential on the subject. Notably around the time of his ordination there was a group of Dominican friars that had arrived on Hispaniola who were so offended by what they saw there that they refused to give communion to any active slave owner. Which for Catholics is a huge problem.

One of these friars, Antonio De Montesinos, gave a passionate public speech that De las Casas witnessed, including the lines: "Tell me by what right of justice do you hold these Indians in such a cruel and horrible servitude? On what authority have you waged such detestable wars against these people who dealt quietly and peacefully on their own lands? Wars in which you have destroyed such an infinite number of them by homicides and slaughters never heard of before. Why do you keep them so oppressed and exhausted, without giving them enough to eat or curing them of the sicknesses they incur from the excessive labor you give them, and they die, or rather you kill them, in order to extract and acquire gold every day."

Notably, this was a controversial position in the church. In fact, the famous Valladolid Debate was a debate between De Las Casas and Juan Gines de Sepulveda (among others) over the moral implications of colonialism and the practices involved with it. Sepulveda argued that the native Americans were not fully human, citing reports of human sacrifce and cannibalism in some tribes as justification to condemn the entire population of the New World. His main argument was that the only way to convert and "civilize" the few who could be "saved" was through European domination of the natives, with whatever violence was necessary to keep them in line. De Las Casas argued that they were rational and innocent human beings in possession of souls, and that they could be converted peacefully. And, that, peacefully converting them was the only moral and legitimate way to convert someone.

By the early 1540s his advocacy had some effect and laws began to be passed, slowly ending the enslavement of the natives and granting them some few protections, along with greatly expanding efforts to convert them and "save their souls".

Ironically, earlier in life, in his desperation to atone for his crimes against the new world natives, De Las Casas had advocated for the replacement of indigenous slavery by importing slaves from Africa, who he had heard were much more robust and generally more suited for a life of slavery. He may not have been the only factor, but when the enslavement of the natives was abolished, and was replaced by the imported African slaves, he felt partially responsible. He felt responsible and almost immediately regretted it when he actually met African slaves only to realize that that were, in fact, ALSO people. He may not have been the deciding factor in the matter, but he had definitely been a loud voice in it, and blamed himself for it for the rest of his life, advocating for the ending of all forms of slavery.

Sorry I couldn't give a more comprehensive answer, as this is a long winded response that only really covers a part of your question. And it's been a number of years since I've read the account (can't find my copy currently) so some of my dates and minor details might not be perfect. But I hope it helps a little.