Don't forget the small detail you're neglecting to mention: That over 90% of their population had already been wiped out by disease over the last few hundred years prior to large-scale European expansion in the Americas. (And it was not intentional! The whole "small pox blankets" thing was in the 1700s, well after most of the deaths had occurred!)

Adding that detail, the situations are a bit more apples-to-oranges.