I can see the Council not wanting to get caught in another drawn out conflict so soon after the Dominion War. Their thinking still seems very short-sighted considering the danger the Eav'oq faces even if they don't want the UFP's help. The First Fedeeration-Klingon War would have turned out differently had the Council considered intervening on Organia's behalf interfering in the affairs of a non-Federation world-- with a pre-industrial society I might add. And it seemed a little out of character for Bashir to have that rigid an interpretation of the Prime Directive, unless he's still in a huff over his last confrontation with Ezri.
All that said, a good cliffhanger. Odds are Bajor doesn't secede, but that last line leaves us hanging by our seats.