They just seemed to give up on Bareil. Originally he was going to be Kai, that was his purpose for being on the show, but when they suddenly decided to make Winn Kai instead they had no more use for Bareil. No doubt they could have given him something to do if they had tried, but instead they decided that he was disposable. I find the episode odd in that Kira doesn't play a big role in the story even though she was supposed to be in love with the guy, the final scene of her sitting there talking to him felt weird because of how she wasn't in the episode much. As for the B-plot, Ron Moore has admitted his mistake in that regard according to the Companion: Interestingly, one of the plans they had for this episode was that O'Brien was going to die instead of Bareil. Colm Meaney was doing a lot of films in Ireland at the time and the producers thought he was planning to leave the show to focus on them full-time, so they offered him this plot as a way out. But Meaney didn't want to leave the show so the writers took the concept and set it around Bareil instead.