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."
If Ira Behr made the claim that Sisko was Half Prophet, that certainly isn't what was shown onscreen. What was shown on screen was that a Prophet possessed Sisko's mother, and influenced her to get pregnant by Sisko's father. Their was no indication the Prophet contributed any Genetic material
Well, it kinda has to be, because otherwise it makes no real sense why they would go through that whole process. Why not simply chose someone who's already born to be the One?