The rule clearly states that to overturn the call, there has to be clear evidence that the ball crossed the goal line before he was down. Seeing as there was no angle that clearly shows that, because you can't see the ball when he was down and can't see the ball cross the line before he was down, the ref did his job.
The NCAA has two choices to improve upon the replay.
1) Allow for an additional challenge by a team once a year, after a replay is inconclusive, for a judgment call to be made by an official approved before the game by both schools.
2) Add censors to both ends of every ball and the front of each pylon to allow computers to graphically show the exact position of the ball in relative position to the goal line at any given point of a play so officials only have to determine the point in which a player is down.