I never bought the publicly stated reason for his resignation, but I'd be shocked if the real reason was the fraternity thing. Speaking as both a fraternity alumnus and small donor to the athletic department, any thinking person understands there's just so much liability there, the University administration really has no choice but to keep those guys on a short leash.
GrayTide's possibility of Fran syndrome is the best explanation I've seen -- maybe the job's simply too big for the man.
Just as Fran's problem wasn't coaching ability per se, it was inability to handle the other aspects of the job, I don't think Bailey's problem is smarts or administrative ability...it's inability to handle the dozens of constituencies tugging on his coat every day.
Some are social, some are political, some are material, and some are laughably trivial. But the President of the University of Alabama has to be able to manage them all, and do it under the close scrutiny that comes with being the CEO of the flagship institution of higher learning in a state that worships its colleges.
Regarding Bonner, I'm undecided. She was never seriously considered for the job when Witt was elevated. Then, just 90 days later, she's the best fit in the country? Please. I think the BoT just didn't have the stomach for another search, and turned to a safe relatively short term solution.