So, it looks like Jose Bautista gets what he wanted, out of the two hole. To me, well if it makes a player more comfortable to hit in a particular spot in the order, why not put him there. If Jose feels it has to do something different (which he shouldn't) because he's batting second, then he might be better off batting third. Or at least it is a convenient excuse for why he's been slumping.
Back in the old days, I thought that Devon White batting lead off was a terrible idea, but then, Devon hit far better in that spot than he had hit for the Angels. So, while Molitor or Alomar or Olerud might have been a better choice to bat in that spot, if it made White a better hitter than he would have been hitting somewhere else, then it more than makes up for it.
If Jose is more comfortable batting third, if he hits a little better there, then, even if the two spot is the 'right' place for him, we might be better with him third. As much as we'd like to try to forget it, players are people and they have their own biases that are hard to get past.
I do think that John Gibbons should have explained to Bautista that, even though he was batting second, they didn't want him to change his approach at the plate. That they didn't want him to bat like a number 2 guy, they'd like him to forget where he was batting. Maybe he did, maybe it didn't take.
The team is having a 'player's only meeting' at the moment. Wouldn't you like to be a fly on the wall for that? It must be a lot of fun and a lot of finger pointing. Mostly at Dirk Hayhurst, I'd imagine.