I have thought long and hard about this. I don't think LSU scoring would have really been that embarrassing - they we're already beating us 52-3. If you run a bunch of HB iso's and score, it's just not a big deal. It's not their problem we can't stop their 3rd string offense. But they didn't. They ran a naked boot leg down to the 1 yard line (he actually scored if you look at the replay), and THEN kneel.
They were trying to score, got down to the 1 yard line and Miles said to Kragthorpe: "Oh my god this is way to easy. Sit on this one."
Another possibility? Maybe Zach Mettenberger was just "Tebowing" on national television.