According to the Bajorian texts, delivered via the orbs, the emissary would save Bajor. The terrestrial aliens/gods knew that there would be an emissary all along. However, when Sisko presented himself, they didn't know that he was the emissary at first and then figured it out.
The religious aspect, Christ-anti-Christ, may be over-the-top for some, but I thought that it worked.
The epic showdown between Dukat and Sisko was pretty damn awesome, IMHO.