What do you mean by pacifist? Did they not have a culture or preparedness for conflict or did they actually have a pacifist philosophy that would prevent them from entering conflict to defend themselves?
They had a philosophy against it - see "Nunuku's Law"
It's also the case that indigenous people killed each other off. For example, the Māori genocided the pacifist Moriori and the Comanche came very close to doing so with the Apache.