Yeah, I'd say your friend has the wrong target there. My experience has been not seeing much mention of Native Americans at all among that culture. Most people seemed to consider a somewhat sad and hopeless topic. But the "other" Indians do get a lot of disrespect from hippies today. Maybe more-so nowadays than in the '60s, but wasn't more than a twinkle in my father's eyes back then, so I can't really comment on that.
Ironically, a lot of leading Buddhist scholars got quite angry with Kerouac and the beats who he introduced to eastern philosophies -- said his interpretation was insincere or insulting (for instance, he was an alcoholic the whole time, which they viewed as hypocrisy). From reading his books, I never got a vibe of disrespect at all, nor exactly one of ignorance... he certainly wasn't malicious or unintelligent. But nonetheless I understand why the scholars were angry. As for hippies today, I have no idea. Hippies today are a pretty sad bunch it seems like.
I can't speak for hippies today, but I certainly was well acquainted with them in the 1990s. I was deep in the midst of hippie culture in Missoula Montana. It was quite possibly one of the leading hippie areas of the US at the time, which was cause for many a cultural collision as most of the state is populated by either Cowboys or Native Americans. The hippies of Missoula in the 1990's were dicks. Uncultured, uninteresting, one-dimensional dicks.