(Lots of interesting stuff)
That's a good way to look at it, I guess. Making it about the war as a whole rather than about the two of them removes the need to assign the dark and light to specific people, which is where I get hung up.
Since trying to assign meaning to the words for some reason makes my brain break, I went back to
looking at the episode.
When she says "A light only shines in the dark," the camera cuts to Prin lying in a shaft of light. Assuming we're being given a clue, I would say that could mean Prin has been living in the dark -- literally -- and now he's in the light, his crimes are exposed and he's been brought to justice.
The only reason I think this might be a red herring is that that shot is also part of the Silence of the Lambs homage, and may not have been intended to be taken that literally.
But let's say it was, then we're back to the idea that Kira thinks he was the dark one, and since she was the one who brought him into the light, that seems to imply that he was bad and what she did was good.
There's also something slightly accusatory about the way Visitor delivers the line. There's a coldness in her eyes when she looks at him that makes it hard to take it as her being sympathetic to him, or seeing them as equals in guilt and suffering.
The words on paper are ambiguous, but based on the way it's shot, I think it leans toward something like this:
"A light only shines in the dark"
(I, the white knight of freedom and righteousness, only became what I am because you evil Cardassians came and did your evil deeds to my planet.)
"And sometimes innocence is just an excuse for the guilty"
(You defended your actions by claiming innocence, but you wouldn't have gotten bombed if you weren't there doing bad things in the first place, but you don't want to admit that you brought it on yourself.)
I think this is the best-supported interpretation, but it's not conclusive at all. The inconclusiveness is what I find so frustrating. What's the point of telling such a character-driven story if you can't figure out what you were supposed to learn about the character?