I think Alabama would have beaten Ohio State, maybe handily.
That doesn't matter. If Ohio State hadn't been banned, it would have been Notre Dame-Ohio State. Alabama would have been playing Clemson. And it's very possible that in that scenario, Alabama would still be the best team in the country. But they would have been on the outside looking in.
Come to think of it, 2012 Alabama has more in common with 1999 Nebraska than it does with any of the national championship Nebraska teams. Stifling defense with a good enough offense, and both teams lost a game they probably shouldn't have lost. The only difference is that Alabama was lucky enough to have it happen in a year where one of two undefeated teams was banned from bowl play, while Nebraska was not so fortunate.
2011 Alabama has more in common with 2001 Nebraska than any of the 94-97 national championship teams. Didn't even win their own division, and yet they somehow stumble into the national championship game, which they didn't deserve. Imagine if 2001 Nebraska had to play 2011 LSU and helpless Jordan Jefferson for the national championship, instead of 2001 Miami, one of the best teams ever. Frank Solich might still be our head coach.
2009 Alabama is the only year they didn't have a mark on their record or require a tremendous stroke of luck to win a national championship. You could compare them to 1997 or 1994 Nebraska, but they weren't as dominant as '95, and they didn't play anyone as scary as that 1994 Miami team, with Ray Lewis and Warren Sapp.