Personally I'd be for pretty much just ignoring it, the same way they do his whiteness. Just avoid those particular places in that particular period of time for a few seasons. No need to make an issue about it just because the Doctor is suddenly a few shades browner. It isn't like his opinion of slavery and racial discrimination is any different now. He would probably just consider it one of the less pleasant quirks of humanity and brush it off if he came face to face with it.