This is probably going to come off as me just defending the Yankees, but I really don't think he intentionally threw at Bay. As immature as Joba sometimes comes off when he is on the mound, I don't think, in a close game, he would jeopardize the Yankees chances of winning.
I've also reached this conclusion because there really isn't any motive in my opinion. He was angry at the umpire, not at any of the Red Sox hitters. I think his reputation is getting the best of him in this situation, but I think it's important to look at whether he had actual motive to intentionally throw at someone.
EDIT: And as for the pole, I didn't vote because I don't agree with either of the options.