The games are not canon, the only things that are canon in the games are the cutscenes. The part where you fight the Emperor, is gameplay not canon...in the novel(which is the canon as the novel comes out before the game) he didn't fight Palpatine. Cutscenes are the only things, that are canon in games.
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.