I feel for the guy and agree with his assessment of the situation. The organization went out of their way to embarrass him and attack him personally as he was on his way out (especially the pain medication accusation)*. Completely unnecessary on their part, and an embarrassing act by any organization.
*Even if you don't agree that the organization (or someone high up in it) purposely released this information, they DID NOT go out of their way to refute the accusations publicly, nor did they return Francona's calls after the story broke.
It will be a shame that Francona won't be there, as he's one of the top-2 managers (possibly the best) in the history of the club. Give it some time - 5 years or so - and I'm sure the bad blood will settle and he'll return for a Francona Day or something of that nature.