You nailed it. Which is why my point is that the official needed to throw the flag as soon as the pass was thrown. By waiting for him to catch the TD to throw the flag, he opens himself up for accusations that he was just looking for an excuse to take the TD off the board. If he REALLY believed Williams was covered up, he'd have thrown the flag as soon as the pass was thrown.
I don't subscribe to the conspiracy theories, I think SEC officials are just incompetent because it's a good ole boys network instead of merit-based. But gross incompetence can lead to accusations of corruption because sometimes it looks the same. Though I definitely think corruption does happen, just not on a grand, organized scale at the league office level.
I think this guy was ball-watching because he's not a good official, and he belatedly remembered to throw the flag after the touchdown because he was so caught up in seeing if the deep bomb would be caught. But he puts himself in the position to be accused of point shaving by not being good at his job.