I used to think the same thing, but I now believe that is wishful thinking.  The Europeans had 10,000 of cultural and genetic adaptation to high density, agricultural based living.  The natives lived a fundamentally different way of life that required far less population density.  Like the Navi in Avatar, most natives would rather fight and die than give up their ancestral ways.  And even if they had wanted to assimilate, it's not clear it would have been possible.  While there was some peaceful co-existence on a small scale, as soon as the density grows the farms start encroaching on the hunting grounds and the conflict becomes unavoidable.