Nope. The dispute still exists. If they win thir bowl games - Oklahoma, Hawaii and Georgia fans will still claim that they got screwed. The only people that universally acknowledge the winner of the BCS Title game as national champion is the media. Since when is the media accurate and when did FReepers start giving a rip about what they thought?
Oklahoma fans would have a legitimate gripe under those circumstances. Hawaii fans would not — since that team never would have gotten a major bowl bid in any era (think of them as the modern-day version of BYU — which didn’t even play in a major bowl when they won the national championship in 1984 with a 13-0 record). And Georgia fans wouldn’t, either — since they lost two games themselves (including one by a landslide to Tennessee and one to a marginal South Carolina team).