IMHO, the closest analogue of bigotry that Federation society could show is against genetically improved individuals. So... what about some augment crew member? Old-type, Khan-series augment; either re-created in XXIII century, or probably from some remote colony, founded long ago by augments that were more sucsessfull in therms of spaceflight than Khan.
Such character may, actually, represent quite interesting plotlines, even within the Federation society. After all, even in XXIII century augmenst were generally threated with a lot of suspicion...