Not really a substantive post, but one of the more interesting things about Cally is something Chief alluded to in that scene where he confronts Baltar's cult: "Cally wasn't like me. She forgave you for New Caprica; she even read your stupid book, but not me. [something about sins even God won't forgive.]" (paraphrased)
For all that she held an epic grudge against the cylons, Cally had a very forgiving heart when it came to *everyone* else. Her cynicism about the "toasters" was matched only by her almost childish idealism about what the human society could be, even in the worst of circumstances. Not only forgiving Baltar, who literally signed her death warrant, and being one of the relatively few people to argue that he should get a real trial; she was also the voice of "we can't start turning on each other" when Captain Kelly was blowing up all the pilots because ... pilots kept dying. (...?) Of course, she firmly believed that OBVIOUSLY it was Athena, DUH. *g* But it's not like the actual truth made any more sense? And I think her reasoning there was similar to what she said in Litmus, when everyone first figured out that the Cylons looked like humans and started to go all Patriot Act: if humans were to survive, they needed to have faith in each other. They couldn't be consumed by conflict or blame or the suspicion that everyone around them was a Cylon. (And again with the irony. D:)
I forget who said once that Cally was often about the US vs. Them, but that was because the Us half of that equation was so important to her. In a way, I think that's part of why she hated Boomer - and by unfair extension, Athena - so much; not just that she shot Adama, or that she did to Chief's psyche what Chief was soon enough going to do to Cally's - but that by seeming to be one of them, a trusted member of the human family, and then turning out to be the enemy, she dealt a heavy blow to their ability to trust and rely upon each other.