Well, if this were Politics, the statement would be bad news, as saying you "stand behind someone 100%" usually means either that your really ripping mad at him or he's about to lose his job (the latter not applicable in this case, clearly). But BB is such a straight shooter that I'll assume he means it.
However, I do ascribe to the old adage that "where there's smoke, there's fire." Given how surprised a lot of "experts" were in the first place when TB went to the Clinic in LA for his surgery instead of a Boston Hospital or a more well known doctor like Andrews, and given the way it's turned out with the infection, etc., I wouldn't be surprised if there were some in the Pats organization who were a little peeved at Tom for not having the surgery done where they wanted it.
I'm neither a Doctor nor do I play one on TV or on this board, but it is my understanding that the procedure that Brady had will fail if an infection destroys or limits the effectiveness of the graft.