Glad you asked. Check out the Nobel Prize winning work by Acemoglu in his book Why Nations Fail. He makes a compelling case that the encomienda system put in place by the conquistadors impoverished South America at the time and continued to impoverish its victims in the future as well.
So yes, extremely evil even by the standards of settler colonialism.
Wait, so you're telling me a system of forced labor where people were sometimes worked to death was bad? /s
What is the counter-factual Acemoglu is comparing against? A scenario where the Aztecs had not been overthrown by the Spanish?