You have no idea the context of what happened. You have no idea the working relationship, or the nuances of what happened from the beginning of his time at Syracuse to when the change occurred. Nobody does. But the way things happened and the sequence of events certainly make me believe the "conventional wisdom of the board" regarding McDonald and his outing his own demotion.
I'm pretty sure if I'm a manager, I don't make a change unless I absolutely feel that its the best decision to make at that given time. Shafer felt it was that time - and he only went public to "embarrass" him once it was already public. Which doesn't strike me as the most direct way to go about embarrassing someone you intend to embarrass (hence conventional wisdom, which is also the most logical).
You really don't have the right to criticize Shafer without also taking into account his side of the deal. No kidding McDonald was upset - anyone would be in that position. But with everything that I had seen from him regarding play calling - as well as public speaking (remember, the " It" article was already out) told me all I needed to know about the success he could or couldn't have as an offensive coordinator at Syracuse. It's possible Shafer saw it the same way.
Also - just because you would manage a certain way doesn't mean that's the end all, be all. Many different managerial philosophies work at many different organizational levels. You may have experience running all sorts of companies, you may even run a pretty big one. I don't really care, and I'm not sure it's really relevant - at least in my opinion it isn't.
Other coaches in the past have done things that were wrong, too. Hiring old buddies to run sides of the ball that they aren't qualified to run is Exhibit A on that list for me.