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"if the European invaders where not evil, ruthless and completely without moral compunction, how were they capable of doing the killing?"That's precisely why it matters who was "evil" and who wasn't. This kind of "pure evil" doesn't really exist, and by assuming it does you are glossing over the real causes of the native genocide. It's far too easy to ask "why did the Europeans murder the natives?" and answer with "because they were evil, ruthless, and completely with morality"
It's a feel-good answer, because moral absolutism makes us all feel better. But it's far from the truth - and masks analysis that can actually help us prevent things like this in the future.
For example (and apologies for the Godwin): we know that not every Nazi soldier was for exterminating the Jews. Heck, we know that many German soldiers guarding the extermination camps were not supportive of the cause, yet they went along with it. Why?
The simplistic explanation that makes us feel better is that these men were evil, without morals, and participated willingly in mass slaughter. But this ignores much more useful insights on mob mentality, the power of coercion, propaganda, misinformation, and a slew of other things that actually help us understand what happened, and prevent these things from happening again.
We're talking about an event that occurred hundreds of years ago - playing the blame game is pretty pointless at this point. It really doesn't matter what is whose fault; the importance of understanding the European conquest of the Americas is to determine the factors that caused a bunch of perfectly reasonable people to exterminate entire civilizations, so that we may better understand our present selves and hopefully prevent such things from repeating.
Which leads back to your original question:
> "Why does it even matter who was "evil" and who wasn't?"
It matters because by playing the blame game, and telling this story as a fairy tale of black and white, good vs. evil, you are bypassing the need to analyze what is, in reality a complex situation of many causes and effects. You are robbing a heinous and dark event of its proper gravity and complexity, and grossly simplifying something that carries relevance today.