The whole Pah-Wraith thing could've still happened without Dukat becoming a crazy cultist.
After he escapes in Waltz, he just comes to the conclusion that the Prophets have to go since they're keeping Dominion reinforcements away. He knows that the Feds would stop any attempt at using whatever type of radiation that kills Prophets on them, so he starts researching other ways and comes across the story of the Pah-Wraiths.
He then pretends to become a crazy cultist to gain favor from the Pah-Wraith worshiping Bajorans, leading us to the Bajoran surgery and seducing Winn for his own purposes.
But then Winn poisons him, and the Pah-Wraiths revive him except the "Anti-Emissary" Dukat is nothing but a possessed corpse.
Sounds good. The key to Dukat is, Dukat is never a "true believer" in anyone but himself. He might pretend otherwise if it suits his agenda, but it will never be real.