I agree as well; A Call to Arms
is one of those cases in which you shrug off the problems because the episode as a whole is just so rewarding.
I also agree that this is the best cliff-hanger episode. Most of Trek's cliff-hangers - meaning the dilemma itself - are quite good; the problem is the structure of the two-piece episode. The first half will set up a problem and then the second half resolves it, which often makes for a weaker second half, because said half has to chart a journey from "event that has the potential to change everything" back into "status quo", and it just becomes an exercise in undoing everything exciting about the first half. Here, though, the cliff-hanger leads into a new status quo, because DS9 has finally built up enough plot threads and character arcs that the show had to go places rather than seek the shortest route back to the familiar and comfortable.
I suppose that's why I disagree with the idea that DS9 is the show about "boldly going nowhere"