Can't remember Bareil ever to reveal the location of any resistance camp. I think that was the thing with Kai Opaka who sacrificed a couple of thousand people (including her son) to save another couple of thousand people. (Or wait, there was something with Bareil. Which was the reason for Winn to become Kai. It's been quite some time since I watched the early seasons.

)
But in "Accession" Kira reveals that Bajor had cast system before the occupation. And they gave that up when it became necessary to fight the Cardassians. So I can imagine that religious rites weren't practised as strict as usual. But I also can't remember that the Cardassians ever banned anything concerning the prophets. They were just interested in the orbs because they wanted to discover the hidden powers.
As for the second question: I think they tried to keep people calm. Meaning that the Kai was supposed to prevent people from doing something "stupid".
Ulli