It's a testament to the strength of this 8-parter that "A Time to Stand" and "Rocks and Shoals" are NOT the strongest segments. You could almost call the Sisko portion "filler" in the sense that it doesn't absolutely advance the main part of the story - except it's so exciting.
I actually prefer the Odo-Kira arc a little better here. You get a very unsettling encounter between Kira and Dukat, with the latter at his creepiest. Quark gets a nice turn lecturing Odo and Kira, while Jake has an amusing encounter with Weyoun. But this is really about two protagonists - Kira and Odo - trying to straddle the line between resistance and collaboration.