I agree that Tony in the mid-seasons was a bit over the top, but I think that he tempered down in season 5. I also think Tony was put in an impossible place at the end of Judgment Day -- he'd obeyed Jenny's orders up to a point when he really knew something was up; he was both worried someone was going to blame him for her death and at the same time was trying to goad someone into saying it just once. And then when Vance kicked him to the curb for what looked like political reasons, it was another heaping tablespoon of badness. Because Gibbs didn't blame Tony (and I don't think Tony or Ziva knew how sick Jen was, and thus her motivation to go out like that) and so if the team had stuck together, Tony would have dealt. But alas.

And man, I ramble. September cannot come soon enough!