The O'Briens' baby was already in danger, as the assassin had proven capable of hitting targets on Bajor and on Deep Space Nine. It had already become clear that once the killer had "made his point" to Kira, she would then be eliminated, so it was more a question of either taking action or sitting around helplessly waiting for herself, the baby and/or more of her friends to get killed.
I wouldn't call it a prudent choice, but it was definitely in character (and not necessarily any more dangerous for the child than remaining on the station). We find out later that the killer might have tried to find a way to save the child, but there was no way of foreseeing that at the time.
Kira's attitude at the end was also in character in the sense that she was speaking as a resistance fighter: all Cardassians on Bajor were members of the occupying force in their minds and therefore legitimate targets. That doesn't mean what the resistance did wasn't horrible. Millions had died and an entire planet had been enslaved. If you are fighting back against that you are not going to come away with your hands clean.
But by the same token, the Cardassian in this episode had deluded himself into thinking that any Cardassian on Bajor not directly involved with the military was therefore somehow perfectly innocent, which is nonsense. You might be a bureaucrat or you might be a mechanic or a cook, but if you are contributing to a crime on the scale of the occupation, even in a small way, you are implicated and partly responsible.
The bottom line is: none of the Cardassians had any right to be there. If you mercilessly conquer a world in an unprovoked act of aggression, then start living there with your family, don't expect the people you have enslaved to be careful not to hurt that family you care about so much. Your family wouldn't be in danger if you weren't living off the spoils of empire. Yet murder is still murder.
Hence the idea that "you can't separate the darkness from the light" which closes the episode: there is no easy way to clearly distinguish between the guilty and the innocent in that type of situation.
Kira is a character with a ruthless side, which is understandable considering her past. Her lack of repentance and unapologetic attitude is one of the things that makes this an excellent episode: she is not sorry, because in her mind she did what she had to do to drive out an occupying power. Obviously, as a viewer, when I am confronted with that attitude, especially in a character that I am able to sympathize with in a number of ways, that makes me a bit uncomfortable. But that is exactly the kind of thing that drama should spend its time doing.