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.
Also, I didn't like the way that they retconned Sisko into half-Prophet. Ira Behr seems proud of that decision, I think it was stupid and changes a lot of early DS9 stuff, like "Emissary."