You say they "only" won by 2 touchdowns... like that's a trifling amount. Outside of video games, message board trash talk, and distant memories of games gone by, these FBS vs. FBS match-ups in which one team "should" win by 7 touchdowns, or was "supposed" to win by 6 scores, are largely mythical ("rarer than some people think" would probably be more apt though), or at the very least reserved for your Alabamas of the world.
In the Sagarin ratings, an average SEC team playing an average MAC team on a neutral field "should" win by 19. I'd caution against trying to apply anything more than that to a Big East team (Pitt) that barely qualified for the conference's very last bowl tie-in, finished the season with a losing record, and was playing on the road. Saying Pitt should have beaten any other FBS team, let alone by 3 scores is a stretch to me. If a team really doesn't think they can stay within 3 TDs of the 59th rated Sagarin team on their own field, then they shouldn't be attempting to field an FBS level football program. Just go FCS where that level of performance would merit some sort of "moral victory." For that matter, an UGA team that finished #4 "only" beat UB by 22!
In truth, I've always believed the entire notion of discrediting a team's win by saying "OK, you won, but you still suck because you should have won by even more, HAHA!" to basically just be an invention of online forum posters to allow them to keep trolling after a loss (and I am in no way saying you're doing that, because you're not, but if you've visited enough sports forums then you know that attitude is pretty prevalent).