I can't speak to explorers specifically, but dominican priests who arrived with the explorers were often openly opposed to the mistreatment of indigenous people. Two notable cases at the very end of the 15th century and the early 16th century were the Spanish priests Antonio de Montesinos and Bartholomé de las Casas.

Antonio de Montesinos was a dominican priest who is most known for his December 1511 sermon against the Spanish explorers. He asked his audience "¿Estos no son hombres? ¿No tienen ánimas racionales?" (Are these not men? Do they not have rational souls?) He didn't pull any punches and, addressing the soldiers and landowners in his church, told them directly "estáis en pecado mortal" (you are in mortal sin). This was not a popular message (for obvious reasons) but it did have a profound effect on Bartholomé de las Casas, who was in the church.

Bartholomé de las Casas was a land and slave owner on Hispaniola (current day Santo Domingo), He was a priest before Montesinos' sermon, but after the sermon he changed his beliefs on the hacienda system and began advocating for the just treatment of the indigenous people. His most famous book "Brevísima relación de la destrucción de las indies" (Brief Telling of the Destruction of the Indies) was written to King Charles I of Spain in 1542. It tells, in short, direct chapters, the horrible things he saw happen to the indigenous people. He includes stories of soldiers raping and torturing the natives, genocide, and backbreaking labor on the haciendas (he had given up his own hacienda before this). Throughout the novel he maintains the question of Montesinos "are these not men" by using language that describes the natives as "souls" "children of God" "creations of the Father." This language was a tool to frame the natives, not just as unknown resources on the other side of the world, but as men with souls who deserved just treatment.

Las Casas get's a little bit of flack these days because one of his proposed solutions for treating the indigenous Americans better was to import African slaves to do their difficult work instead. He did come to regret that suggestion and publicly recanted it (and apologized for it in his book "History of the Indies").

Sources:

Texto del sermón de Antón Montesino según Bartholomé de las Casas y Comentario de Gustavo Guitiérrez (Text of the sermon of Antonio Montesino according to Bartholome de las Casas with Cometary by Gustavo Guitierrez - Spanish pdf is available online)

Brevísima relación de la destrucción de las indies de Bartholomé de las Casas (Brief telling of the destruction of the Indies by Bartholomé de las Casas)