The problem is that you are actually understanding that conflict less, by painting 16th century Spain as how you'd like it to have been.
For example, the Spanish crown formally accepted the natives, since the return of Columbus, as citizens of the crown subject to the same protections a native spaniard had back then. Very liberal for the century. It's just that the landlords (caciques) were much more seduced by the idea of free labour, and there was no government oversight on the vast, new-found lands.
Similarly, the Company of Jesus were a religious order which instructed the natives, built schools, advocated for the end of all slavery, and protected natives from exploitation at hands of ruthless Europeans. Hardly crusaders or templars.
But sure, if blind prejudice derived by generalization makes you feel superior...