I highly doubt that the Jedi pieces based on the game will be Rebel faction.
First of all, it doesn't fit the continuity of the Saga. The 'Rebel Alliance' as we know it Episode IV started not very far before the beginning of Episode IV. Granted, information about the game seems to suggest that the game events will lead into Episode IV, but we don't necessarily know in what capacity.
Secondly, putting characters like Shaak Ti or Quinlan Vos into the Rebel faction just doesn't fit the playstyle of the Rebel Faction up to this point. Up until now, creating a good Rebel squad means you pretty much always are including at least one or two characters from the original triology (Luke, Han, Leia, etc.). General fans of the Rebel faction and the OT may hardly even know who Shaak and Quinlan are. IMO, it just doesn't make sense to put them in the Rebel faction.
On top of all that, if I was a Jedi that was surviving in hiding throughout the Purge period, I think I would be pretty set on helping defeat the Empire in order to bring back the Republic. Sure, that's basically the idea behind the Rebel Alliance as well, but the Alliance's goal ended up being just defeating the Empire to get rid of them period. There wasn't really a plan on what to do afterwards. I think anyone from the Republic era would desire to put things back to where they were before the Clone Wars.
Granted, it's all just speculation. And with two, possibly three EU heavy sets coming next year, it wouldn't surprise me too much to see this one be another OT heavy set. I just hope that isn't the case. At least I can't read the WotC forums much now anymore, so I really won't have to worry about hearing all the griping about more OT characters when we just got a bunch.