Well yes, though, I am definitely not sure how Christian kill Native American ? Wasn't it not more a matter of expansionism, land grabbing, and more importantly, railroad companies ? Was religion really involved in native american history ?
The Spaniards went full Amarr on the indigenous peoples of the Americas, killing millions, raping and pillaging, and utterly destroying their societies. The priests gave them a pass as God's will, and blank cheques to murder any who would not convert.
Sadly enough human nature being what it is, the greedy Spaniards listened to what they wanted to and ignore what was inconvenient to their profit motive and denigration of the other, including the parts of religion that were inconvenient.
The following condemnation of slavery was not from Pope Franchis I, or even a more "modern" pope but Pope Paul III who issued a Bull against slavery, entitled Sublimis Deus, to the universal Church. He wrote:
...The exalted God loved the human race so much that He created man in such a condition that he was not only a sharer in good as are other creatures, but also that he would be able to reach and see face to face the inaccessible and invisible Supreme Good... Seeing this and envying it, the enemy of the human race, who always opposes all good men so that the race may perish, has thought up a way, unheard of before now, by which he might impede the saving word of God from being preached to the nations. He (Satan) has stirred up some of his allies who, desiring to satisfy their own avarice, are presuming to assert far and wide that the Indians...be reduced to our service like brute animals, under the pretext that they are lacking the Catholic faith. And they reduce them to slavery, treating them with afflictions they would scarcely use with brute animals... by our Apostolic Authority decree and declare by these present letters that the same Indians and all other peoples - even though they are outside the faith - ...should not be deprived of their liberty... Rather they are to be able to use and enjoy this liberty and this ownership of property freely and licitly, and are not to be reduced to slavery... [Ibid., pp.79-81 with original critical Latin text]
Pope Paul not only condemned the slavery of Indians but also "all other peoples." In his phrase "unheard of before now", he seems to see a difference between this new form of slavery (i.e. racial slavery) and the ancient forms of just-title slavery. Unfortunately, the kings of portugal and spain disregarded that as well as the bulls from Popes Gregory XIV (Cum Sicuti, 1591), Urban VIII (Commissum Nobis, 1639) and Benedict XIV (Immensa Pastorum, 1741).
There's a good movie that explains the unfortunate interplay between state power, politics, religion, and the priests on the ground called "The Mission". Human history.. is complicated.