even so, in this world banning the worship of one of the major deities is going to have a larger effect that you'll imagine. the thalmor probably demanded for this condition for a very specific reason other than just furthering the destruction of humanity. alduin being the dragon god of time and them doing this to talos seems pretty specific in regards to timing. they've prepared this, probably for hundreds of years. if the emperor had instead strenghtened the belief on talos reaching out to the other countries not as emperor but as fellow man and for men's survival the unison of the countries against the could have been possible. we can't say who would have won, as he didn't even try.
He tried, but the Empire was losing the war. It was evident that they were going to lose the entire war soon, that's why they had the Concordat of White Gold.
True that banning of the worship of a god has a huge effect in the world of TES, but the effect is on the God. According to one of the books in Oblivion, not sure if it was Gods and Worship or some other book, the Gods themselves don't often interfere in the events of mortals. If the Emperor was a Septim then things might be different, because the Septims were blessed by the Divines. The loss of Talos may have strengthened the Thalmor, but it didn't weaken the Empire much. It's not as if Talos worship was the factor that held the Empire together; neither was Talos doing anything to help the Emperor because he isn't a Septim. There just isn't any evidence that Talos was helping the Empire in any way.
However, it might be possible that strengthening Talos worship might increase his power to a point where he can create an incarnation of himself to help the Empire win the war. Maybe this is the Dragonborn in Skyrim. Maybe there isn't such an incarnate. However, you should be able to see how huge a threat to the current Emperor an incarnate of the greatest Emperor ever to exist appeared; everyone would prefer that incarnate on the Throne.
The Wall of Alduin said nothing about the banning of Talos worship; thus it was probably not part of the prophecy predicting Alduin's return. The civil war, however, was part of the prophecy. If anything, perhaps the banning of Talos was a factor which the Thalmor used to ignite the Civil War in Skyrim.