There’s a shock. 
I think I can sympathise with and understand some of her actions.
Let’s look at some of her history which is used against her:
I so want to hate her, but your explanations make sense. You’ve destroyed virtually any logical reason to despise her, leaving only the utterly irrational distaste I have for her. Damn you. Damn you and your cogent arguments. :rolleyes:
So, really, the only ‘bad’ thing here could be the killing of Cally. I’d suggest there were quite some mitigating circumstances: self-defence, saving of Nicky, likely saving of fellow Cylons, perhaps even a feeling that her destiny was to be more significant than Cally’s. Not a perfect excuse, I admit, more of a justification.
Again, I have to agree. Since the four of them would most likely get imprisoned (if not 'locked themselves), there is a certain level of self-preservation that justifies her actions. On the other hand, that doesn’t explain why she waited until Cally woke up to open the door. That was evil. Even if she felt justified, she doesn’t seem to feel any remorse for murdering an innocent woman. So, yeah, that’s more than enough reason to hate her. Consider yourself undamned. 
But remember, plenty of others on Galactica have committed ‘crimes’: the kangaroo court members, Baltar, Lee, Anders to name a few. Some seem to be able to accept these all far easier than Tory.
Military and governmental decisions always seem to be easier to rationalize than individual self-preservation. The needs of the many and all…