I think she felt betrayed by Adama, but most of all I think what affected her was the realization that, while Lee always told her how horrible Adama
was, Kara had always pretty much idolized him, and this was when she realized she was just as biased as Lee, if in the opposite direction.

But what I really don't get about this scene is that Kara's randomly wearing all that lipstick and eyeshadow and false lashes, at a level NEVER matched anywere else, even Colonial Day. What's up with that?