Obama is head of the executive branch. It's his job to enforce the law. If there is a legitimate anti-trust case with the BCS (I think it's obvious that there is), he is supposed to address it.
The government can do more than one thing at a time. True that there are more pressing matters at hand. However, CFB is a multi-billion dollar industry that affects substantially every state in the country. They aren't talking about "controlling" how the BCS works. Only investigating potential anti-trust violations. How they reform (if they are required) will still be up to private parties as long as a new form falls within the law.