Then Kai Winn goes rogue and decides to stop the Reckoning from happening. Why does she decide to stop the Reckoning?
I think this one can be answered: it's because she is jealous that Kira was chosen by the Prophet instead of her.
It came across to me like they were trying to imply Winn did it because of her jealousy of the Emissary's faith in the prophets and his willingness to trust them with his son's life. Which doesn't quite make sense.
Winn being jealous the prophets chose Kira makes more sense, but I didn't see any suggestion of that motivation in the episode itself.