You are incorrect. First the specifics arthurus. Not microbes, but smallpox. Also, Aztecs and Incas, not "south Americans and Mexicans".
And now the generalities - the conquitadors specifically went after "gold, glory, and God". Read about the pope's role in it
http://iweb.tntech.edu/kosburn/history-499/the%20Spanish%20in%20the%20Southeast.htm
Smallpox is microbes just like any other virus or bacterium. And the point is that the indians were not killed off by genocidal massacre. The conquistadores had no notion just how deadly their invasion was until it was done. Aztecs were one relatively small ruling tribe in Mexico which country was named for them- The Meshica Aztecs. They were tyrannical in their rule, even by Mexican standards of the time and their cruelty got themselves offed because their subject peoples, the largest group of which was the Tlascalans, sided with the invaders. The Incas were not even a tribe. They were the rulers and by extension, the ruling class of one Quechua speaking tribe that originally came to power over the other Quechuans, then their neighbors, the Aymara-speakers, and then many tribes up and down the west coast of S. AM.
As for the three "GS" the conquistadores went for the first two. The friars and priests that accompanied them mitigated their barbarity to some extent and the Pope declared the Indians to be Human Beings which prevented the wholesale enslavement of the population. The Indians were not killed for their lack of adherence to the Faith but were exhorted, hectored even, to convert. It was the Pope who made it a requirement that the Indians be treated as human and not massacred or enslaved as animals. He put them under the protection of the Church. They were to be persuaded to convert, not killed and they were not presented with the Mohammedan choice of death or conversion. The Indians in Mexico, at a certain point took the religion of the conquerors. In Mexican culture that is what happened when a new conqueror arose. His god(s) was deemed to be the conqueror of their god.