I've come to understand that Gene saw DS9's concept before he died, and he basically OK'd it. Now, in the early seasons, Sisko's attitudes are ambiguous at best with regards to his Emissary role. Those wormhole aliens just might really be those Prophets from the Bajoran religion, or they might not. Sisko hadn't really decided if this Emissary stuff was for him , but he decided to go along with it for the time being, as his prime role was to get the Bajorans ready for assimilation admittance into the Federation. In the later seasons though, it seems he came to accept his emissary role more unreservedly and accept more of their guidance in his life, even though he still did not always agree with the Prophets' viewpoint. All the same, the "Prophets / just a wormhole species living outside of linear time" ambiguity never really was resolved. (I'm not saying it should have been, just that DS9 always left room for both viewpoints). Now, in TOS (and TNG) where his influence was strong, 'Gods' usually get unmasked as being counterfeit- though not always. What do you think he would have thought of this gradual evolution of perspective?