Another idea just come to my mind: if the emperor is on coruscant, and at the beginning of the movie we see vader arrive on the capital, welcomed by jerjerrod. Jerj could be the moff controlling the coruscant sector or something like that (the regional governor?)

well, we could have riots on coruscant from the beginning of the movie, this could be the starting point of the film. The rebel going there to help the insurgents and finally end the war. Stormtroopers are dealing with the people revolting and then jerjerrod receive the command to fire on both the civilian and *his* troopers, causing him the conflict we see on the deleted footage.