It wasn't an ideal finish to an otherwise great season, but when you lose that convincingly all you can do is tip your hat to your opponent and then do what you can to make sure it doesn't happen again next time. Considering that this was still supposed to be a rebuilding year for Notre Dame, going 12-0 before losing to the team that has won 3 of the last 4 national championships was a successful season by practically any measure. Further, while Notre Dame had some fortunate breaks during the year, so did Alabama, and I think that ND would have had far better chances to win against Georgia, LSU or Oregon.
Turning to next year: we're losing Manti T'eo, but with the #1 recruiting class in the country for 2013-14 the Irish should be in BCS contention for some years to come, and I'll be obnoxiously rooting for them (half tongue-in-cheek) every step of the way!