As sprack notes below, FSU has an arrangement with the local Seminole tribe. They're clearly not named after the Oklahoma tribe, so it seems like they've taken reasonable measures. Illinois's Chief Illinek was misguided, perhaps, but probably well-intended. North Dakota (Fighting Sioux) and Central Michigan (Chippewas) I think honestly intended to honor the history of their region, and in Central Michigan's case the Chippewa tribe's chief actually pleaded with the NCAA to let them keep the name.
However you feel about all that, I think there's a pretty clear line between a team calling itself the Seminoles, Illini, Sioux, Chippewas, etc., and a team having a mascot named "Chief Wahoo" (Cleveland Indians) or a team being named the "Redskins." Imagine if there were a Chicago Taigs franchise or an Atlanta Niggers franchise - in my mind, at least, this would be essentially the same thing. "Redskin" and the "red man" were terms born of disgust and moral superiority, much like "black savage." It really is pretty ridiculous that they still carry that name today.