You could basically mod out all the dream scenes with the Emperor and the story would remain intact for the most part with the prism simply being an artifact that shields from illithid influences. The only thing that would probably need a rewrite is the Gith creché scene and the final dilemma.
Yep, the emperor is basically a plot device that could be removed from the game at this point. Even on the playthrough where my character got him to drop the mask, and there was no trust left, even when the party obtained the hammer, the emperor still acted as if they were all working together. I think even his ending speech was the same. They could have at least restored Omeluum's ring to its original function, so that you can skip the rest of the emperor cutscenes after the prism fight, it's not like they matter.
