Just because Kira was able to forgive other Cardassians for their mere presence on Bajor (Tekeny Ghemor, the Cardassian from "Duet,"), does not mean that, at the time of the occupation, she would have hesitated to blow their asses up. None of the Cardassians should have been there. They raped her planet and decimated her people. Just because Prin wasn't actively murdering Bajorans doesn't mean he wasn't responsible. He passively endorsed the Occupation just by his presence on Bajor. Hey, I'd want to off they guy that hemmed pants for the Nazi soldiers too, you know (or whatever menial job Prinn did). Also take into account that Prinn had just killed her friends, and I can understand why she wasn't in a very forgiving mood.
As for endangering the O'Brien's baby, the argument could be made that the baby was already in danger, and Kira waiting around like a sitting duck would only make her and baby an easy target. How was she to know Prinn would spare the child?
The whole theme of this episode is: can you really separate the darkness from the light? Is any Cardassian who lived on Bajor totally innocent, or are they "darkened" by the occupation? Are Kira's actions, and the actions of her comrades, completely justified, or are they "darkened" by the taking of lives? Maybe it's not as simple as night and day, black and white. Maybe there's some gray.