The "had they joined, they'd be dust" card was well played. No mortal could predict with any certainty that not joining would really protect the planet - but the Prophets would have the predicting bit down pat.
Still, playing that card would have been so much better had there ultimately been a second opportunity for Bajor to join and the planet would have taken that. Preferably with a guest appearance by Picard to boot. Perhaps just a snapshot in "WYLB", a short flash of Picard shaking hands with, dunno, Shakaar, and extras applauding, with no real comment from the DS9 heroes for whom things like friendship and trust now mattered more than words on a paper.
Or then an actual plot moment, showing how Sisko finally achieved what he was told to - say, the no longer mortal Emissary bellowing to the Bajoran government from the heavens or whatnot, or then sending a note via Kasidy, what-have-you. But I'd have preferred the subtler approach, showing that the joining no longer was a big deal. Not showing any joining actually made the opposite impression - that it perhaps for some reason still was a big deal, but one to be avoided for in-universe reason X, not to mention studio reason Y.
Timo Saloniemi