Having the "sins of the Taurus Reach" brought up so far in the future doesn't really bode well for events in the intervening years.
Not necessarily. Some cultures today have long
cultural memories, where the slights and evils of the past centuries gone are still present for them today. Look especially at Middle Eastern cultures, where a schism over a millennia ago still causes trouble between Shia and Sunni. Just because the Tholians, as a whole, may have made peace with the Federation (hence, embassies), individual Tholians may still harbor grudges and resentments against the Federation that go back centuries.