Roslin/Cottle/Tory are in one way easy targets, but in another way, expressing her anger and forcing her friends to choose between her and them, that might not end well. After all, Adama and Roslin were closer than ever within a few episodes (and Helo was behaving himself in a staff meeting at the end of Rapture that would've taken place maybe a day or so after the re-re-kidnapping). And Cottle's the only doctor on the ship. When Hera gets sick, Athena has to take her to one of her kidnappers, at the scene of the crime, so to speak. She's probably got all this anger that she daren't express, and the only safe targets for her are Cylons. Plus, the more anti-Cylon she is, the less likely she is to be rejected by the Colonials. And the idea of rejection by her new people would be doubly terrifying because she's given up so much to get to this point, including almost two years of her child's life. The Colonials CAN'T brand her just another Cylon now, or maybe everything she suffered the past few years wasn't worth it.
And granted, things probably would've been even worse if she'd gone home, and she wouldn't have had Helo. But from her POV, she's clawed her way to where she wants to be, and cut out huge chunks of herself to get there. And along come these Cylons who want what she has, to ally with the Colonials, but they HAVEN'T had to suffer for it like she has, so how dare they try to take what's hers? They haven't earned it.