The initial conquests and the immediate atrocities that followed them (arguably the worst period) were mainly quasi private enterprises. The state even tried to reign them in to some extent due to significant social/religious pressure at home. Of course that was largely superficial and hardly enforced after boatloads of silver and gold started arriving.

The priests and missionaries that followed them were likely the group that was most sympathetic to the natives (of course only in relative terms compared to the "conquistadors" which is a very low standard).