I think it would've been more interesting if Dukat wasn't a true believer, just a vessel for power. If he realized that Sisko commanded the Bajoran Gods and to destroy them is to destroy Sisko's power. He is just chasing the power to control, and beat, Benjamin Sisko because he is emissary.
The final showdown was weak. It's like the writers just wanted to have a reason for their to be an emissary in this time of the series. I thought guiding Bajor after the Occupation was reason enough; that he would bring peace to them. Really, the idea that Sarah had a child with the prophets--the whole story arc for the emissary in season 7--wreaks.