And the Pueblo did appear in American Conquest for example. I don't remember if they were in the campaign however, or just in the skirmish mode.IIRC, the reason the Pueblo didn't want to be represented was because the leader Firaxis wanted, Po-pe or something, was revered by them, as are just about any other good Pueblo leader choice. So it wasn't necessarily about sticking it to European-Americans, but rather that the nature of inclusion in the game violated their cultural values.
So it doesn't necessarily preclude any other Native American group from being included in the game. Remember, they added the Shoshone in response to not getting the Pueblo approval.
And there are some South American groups that really don't want to appear anywhere. I think Microsoft clashed with them over the translation of Windows into their language for example.