Then how, pray tell, do you explain the words of Hall Hood? Which state the exact opposite of what you are saying.
Please, do you really think any writer is going to spoil the story (or future story), the Emperor is someone that they will probably bring back for some expansion in SWTOR don't believe everything you hear even if he wrote the JK story especially if its not confirmed canon. The email the Wrath gets from The Hand states that the Emperor is alive and recovering from losing his main voice, That email is C-Canon due to it being in SWTOR.
Could the Emperor be defeated by the JK in the future, Yes im not ruling that out. All im saying is dont take the writers word when its not confirmed as canon, where the email stating the emperor is alive by the Emperor's hand is C-canon due to it being in the game.