You have to wonder what kind of revulsion they witnessed to cause them to want to wipe most all of them out. They should have, morally before The LORD, witnessed Jesus Christ to them but they seemed like they were propelled by seeing a culture that was so utterly depraved and wickedly blood thirsty that they lost control of their senses and wanted nothing more than to rid the earth of them as quickly as they could.
Others may believe that they had largely different motives but my gut reaction tells me that they couldn't mentally cope with what they witnessed about how the people lived, and how they were ritualistically murdered.
It was not deliberate genocide. The Spanish didn’t understand the disease they carried with them. And it was not in Spain’s interest to see them die off since they wanted to enslave the population. When the Indians died, they were replaced with Africans.
It was European diseases that wiped out the population. It was inevitable.
The Indians did not have the antibody resistance needed to fight very common European diseases. This would have eventually happened whether it was Indians coming to Europe or Africa, or ( as happened) Europeans going to America.