It definitely affects the degree to which it hurts them and pushes it towards the negligible range. If GT goes undefeated we WILL be ranked ahead of Bouse in the BCS, regardless of the polls. Boise will not steal an at large BCS spot because it was going to take on eanyways anyways.
So the only scenarios where this hurts GT that I can see are:
If there are 2 non-BCS teams there and Boise State is taken ahead of GT as an at large when GT would have gotten an at large otherwise.
GT loses 1 game and finishes number 3 in the BCS behind an undefeated Boise (not very likely).
GT misses out on the MNC bases on SOS because of the Va Tech loss or potential bonus points from Va Tech being highly ranked.
GT goes undefeated and somehow the loss indirectly hurts the pollster's perception of the ACC enough that they vote GT lower than they would have otherwise had Va Tech won. If the other undefeated teams are from the Big 12, Big 10 or SEC it wouldn't matter. So one of the other undefeated teams would have to be from the Big East or the PAC 10
Any other ones?
Yes it potentially hurts, but in reality the specific scenarios where the Va Tech loss hurts are so unlikely and there is so much more football to be played that I still disagree.
However, scenarios where it helps:
GT is head to head with VT for an at large berth or GT, Miami, and VT are in a 3 way tie because GT beat Miami, Miami beat Va Tech, and Va tech beat GT. In this case the tiebreaker is the head to head of the two highest BCS ranked teams, which if these were Miami and GT and Miami was no more than 5 BCS spots ahead of GT, GT would go to the ACCCG and have a chance to automatically qualify.
It still does not fix the fact that VT losing to Boise State last night hurts GT. There was not a good result for GT last night. Unless both VT and Boise lose more games and make it irrelevant.