it dealt with religion yes, but not in a way that applies well to real-world ways. As others have pointed out, Bajor's "prophets" were actually powerful energy beings that did intervene in galactic affairs, so the whole "faith" issue is discarded. You don't need "faith," you saw them make 2800 Dominion ships disappear.
To some religious people though, a god did actually intervene in several ways in the past.
Yeah, but there's no proof.
The Bajoran's have the tears of the prophets, which are obviously real and obviously have the abilities of giving you visions or making you travel through time. Their "religion" is very much grounded in reality. They KNOW their gods exists, instead of simply believing it.
The religious part chimes in when they decide that the wormhole aliens are their gods and that they need to worship them, even though the Prophets don't care if those folks visit their temples or not.