Native Indians had already killed each other before the first European step foot.

https://www.theguardian.com/world/2017/jul/01/tower-human-skulls-mexico-city-aztec-sacrifices

Contrast the above story to when the Spanish arrived, who ended up intermarrying the people they subjugated.

So to answer the OP, I don't think there was ever a grand conspiracy by Europeans to eliminate other races they came across.

If the Indians died, it's the same way they're dying for thousands of years. By their own hands or backwardness...