Is it possible that Alabama just out-helmeted Ohio State? Doesn't happen much, but it may have happened here.
Still, Alabama has some quality wins and one quality loss (in the sense that Auburn is very good). Ohio State wasn't that competitive in its loss to Oklahoma (similar to Alabama's loss to Auburn), but was embarrassed by a mediocre Iowa. I don't think the decision was that hard for the committee. The biggest helmet of them all (currently) with one loss to a good team, versus a top tier helmet with two losses, including one bad one.
Yes, the two-loss team was a conference champion, but be honest: the committee doesn't really like Wisconsin that much, and Penn State's two consecutive losses took the luster off the Ohio State win there. The committee just wasn't that impressed with the Big Ten championship. A one- or no-loss team would have been in, but not a two-loss team over Alabama.