A "Western" that treated cowboys and Indians in a non-stereotypical or non-racist way probably would be considered a period drama, not a "Western." This may be a path already started by Deadwood, but I haven't seen any of that. The thing about period dramas is that there's lots of periods to pick from.
Almost anyone picking the US West circa 1848 to 1890 is probably attracted by the Western racial mythology to start with. Anyone interested in US/American Indian relations would find Tecumseh, or King Philip, or Handsome Lake, or the Pequot War or any number of other fascinating stories. The other Western tropes either have modern counterparts, lawman vs. chaos in particular. Or, they are now very remote from modern experience, like cowboy vs. settler, or cow vs. sheep (rural experience was still much in living memory fifty years ago.)