Considering all that Galactica & Co. have been through, it's easy to understand that the chain of command has gotten a little muddled and wonky. After all, hasn't Apollo openly broken with Adama at least twice? Adama has been very forgiving with his crew, because they're a good crew, doing their best. And on the flip side, in other circumstances Gaeta and Doualla would have been promoted long ago for their extraordinary service. In other words, it's getting the point where everyone's the same rank, underneath the Old Man, and they do their jobs not because of military discipline, but because that's what they're good at, and they have to to keep the race alive.
I mean, think about it. D doesn't have to take orders from Apollo if she doesn't want to. Nobody has to listen to Tigh unless Adama makes them. Helo's in the XO slot on Adama's suffrance, and Tigh will slide back into that slot if he's willing because Adama wants him there. Starbuck doesn't take orders from anyone except Adama, or at least there's always the off-chance she won't follow them, and on one or two occasions she's avoided Adama's command as well...
In other words, Adama is God -- all else is negotiable.
(May I briefly express my frustration that the first time I'm actually able to watch an ep live, it's not on the air? Ah well.)