You're probably getting tired of hearing this, but I cannot believe how well thought out and how well written that was! Based on all the evidence given so far and information given about both sides, I believe that Sourge was probably mistaken. The most convincing piece of evidence for me is that the vision he saw was not fulfilled.
Also, in the end of the Jedi Knight story, at the victory ceremony, Scourge says he will stay for however long it takes him to snuff out all of the Emperor's final tricks. If he's as good as the game and Revan novel have described him as, he may eventually discover that the one they killed was merely the Voice. This discovery could lead to the expansion of the story you were talking about (like you, I have no clue how BioWare plans to incorporate this new part of the story).
Also, in the novel, it is said that the "true" Emperor is a Sith Pure-Blood with completely black eyes (I'd quote if I could, but I don't have the book with me). If this is true, we have an idea of what the true Emperor looks like. If this is but another Voice, the Emperor will surface again...some day. Considering the possibilty of the Black-Eyed Pure-Blood being the true Emperor, well....that's obvious, the story isn't over and you keep looking for him. Continuing the possibility that the Black-Eyed Pure-Blood is another Voice, the Emperor may surface again quickly or maybe not for another century...perhaps even more considering the fact that he is technically immortal.
My theory is that the war may end without the Emperor ever rising until long after it's too late. Power struggles and attempts to gain the throne most likely tear apart the Empire, leaving it defenseless against the Republic (repetition of history, just like the Great Hyperspace War). Perhaps thousands of years later, after the fall of Palpatine's Empire, the end of the Yuuzhaan Vong War, etc. the Emperor will surface again and a new chapter in Star Wars Chronology will begin.
P.S. Pardon me if my message and/or quotes seem, "noobish" or unprofessional. I'm new to posting and commenting on forums. Many more apologies if I accidentally repeated a few things that may have been discussed by other people earlier.