Please do not take HN threads further into nationalistic or (god help us) religious flamewar. It's not what this site is for, and it destroys what it is for.
The Inca were probably the most astonishingly advanced Native Americans, and they surely had great thinkers (definitely great engineers). And here come the conquistadors, rock-headed barbarians from the most desperate segments of Spanish society (little else drove people to risk their life for riches in the New World), absolutely slaughtering them, burning their cultural artifacts or melting them down into ingots when applicable.
It's like if (a much more desperate and destitute version of) the January 6th protesters were sent to conquer new worlds.
As an aside, a colorful example[0]: they lured the Emperor in a plaza (he came to show he was unafraid, and his army were disarmed of all but ceremonial weapons), and, in the slaughter that ensued, they tried capturing him. He was up on a palanquin, carried by servants. Unable to reach him, the Spanish began cutting off the limbs of the servants, who it's said, without thinking, bore the load on their shoulders instead (it was unthinkable to do otherwise, as they considered the Emperor a god). Eventually, they captured him. In captivity, they taught him to play Chess, and I think it's said he was good at it. Later, panicked that an army was going to come and re-capture him, they killed him. Before his death, he was offered conversion to Catholicism, which he accepted, which awarded him the clemency of being strangled instead of burned alive.
This is a very colorful view of history. You can also see that the first university in America was built by the spaniards. The first university in Asia? Also, built by the spaniards.
The earlier ships were a mixture of those "barbarians" as you mentioned, and very learned people.
The concept of international law and human rights started with the discussions in Spain after the discovery of America:
https://news.ycombinator.com/newsguidelines.html