I agree that it was politically honest. Terrorism is a form of political violence even though that violence can take on a life of its own and be committed for its own sake. "Past Prologue" contrasts Kira who has given up violence to work within the political system, with Tahna who is still killing Cardassians in the absence of any reasonably obtainable goal. "Shakar" further shows her to be unwilling to kill fellow Bajorans and start a civil war, even against Kai Winn.

I like Kira as a character and I think she was thrown into a terrible conflict as a young girl and showed remarkable fortitude in being able to move beyond that. My main point though is that the show never really confronts in a direct way some of the horrible things she did. She calls herself a terrorist and there are some allusions here and there, but mostly we're given an image of brave Bajorans gunning down jackbooted Cardassian thugs.

"The Darkness and the Light" comes along and gives us a glimpse into the much darker reality of the war she fought, in which civilians and even children were targeted. It comes right up the point of indicting her for these actions but then it hand waves past the reality of what she did with the assertion that the rightness of her cause absolved her of any guilt or responsibility for murdering innocent people. I wasn't looking for her character to be beaten over the head by the narrative and spend the rest of the series self-flagellating; but I think there was a missed opportunity for a morally grey message that wars (especially ones with an internecine element) dehumanize their participants and make them a party to monstrous crimes. The idea that almost any action in the name of one's political community is justified, is a very enduring and a very dangerous one, which whitewashes the actual act of political violence with notions of patriotism and portrays the victims as "enemies" who are little more than inhuman objects to be brushed aside. Star Trek is generally willing to challenge such notions, but I think that this particular episode and DS9 as a whole shrunk from that task.