I'm not saying that the episode needed to focus on the discovery of the Celestial Temple, but the fact that the wormhole is mentioned several times in the episode by Bajoran characters, but they don't mention the religious significance of it is very strange. The fact that a Bajoran came up with a plan that involved putting a massive bomb in the wormhole, and another Bajoran that's trying to stop him (and who we find out later is deeply spiritual) doesn't bring it up is beyond weird.
Take In Purgatory's Shadow as a counter-example. When Sisko plans to close of the wormhole, Kira immediately questions what would happen to the Prophets and Sisko assures her that the procedure would do them no harm. That's the way to do it, not to ignore it like Past Prologue did.
I think Kira became steadily more spiritual as the series progressed. I mean when she was fighting the Cardassians in the occupation was there were really any time for her to sit down, and pray, meditate, or engage in spiritual matters? I don't think so. She discovered her pagh, after the occupation, but I think faith in the Prophets came later.