The video I provided earlier includes a final cut-scene which clearly indicates that he have fought and defeated the Emperor. Here is another video that has no gameplay: http://www.youtube.com/watch?v=Y3T2Z-1spT8
I am not going to discuss Force Unsealed any more because it just brings back the bad memories.
Now speaking generally. Cut-scenes or not, if the game forces you to fight someone then the details of the fight are player-specific and varies (not canon) BUT the fact that there is a fight makes it a part of the game storyline. And the story of the games have the same canon weight as the novels.