LSU is the SEC champion so that is what should matter, as it is more of a trump card in this case for me. Bama would have to beat LSU pretty bad for them to be truly able to hold it over their heads. We are speaking about Bammers, so they won't see it in a humble way.
The way the SEC is right now compared to the state of all of the other conferences, the SEC Championship is by far more prestigious than the BCS championship IMHO. Bias..sure, but it's tough to argue differently at the moment.