I appreciate your observations, and I think that the teamwork thing really is a big factor in this, but I think Wade summed things up pretty well. Matt's reaction to 9-11 is scorched earth, and while that's devastating, it happens.
I really think Matt could have worked the team thing out with Wade with some better communication. Explaining that he'd change his ways, but at the same time telling Wade how he felt about quitting the team, and fulfilling his leadership role, would have resonated.
I agree with you on Will as well, but I'm also going to give him the 9-11 crisis bye, and acknowledge that, rational or not, this thing with Matt and Tony is an open wound. For Will, Matt's action is like a big "fuck you" to him, and makes Matt's original apology seem as meaningless as he feared it was.