I actually wouldn't be surprised if the NFL had asked the mics to be off. Remember, this was the first time a female was headlining since Jancel's wardrobe malfunction and everyone was talking about what controversy Madonna might try and create. The NFL imposes many restrictions, maybe they didn't want anything appropriate to be said. The other guest artists aren't singers who usually lip sync either so it seems weird to me.
Anyways, I wish she had sung a bit live... Or that she would have used a more realistic track. It would have added to the greatness. :)