I've always thought that a game that didn't have some kind of dark Jedi or Sith simply wouldn't feel very Star Warsy.
Luckily, despite the way Return of the Jedi plays out with the absolute defeat of the Sith, and the later retrofitting of the "rule of two", I think there's an easy way to bring them back into play several years after Jedi ends.
Palpatine/Darth Sidious/the Emperor seems like a consumate planner. He's nothing if not prepared for contingencies. Heck, he's even obviously tried to replace his apprentice with his apprentice still standing right there listening to his every word! I actually find it difficult to believe that he didn't have some sub-apprentices waiting in the wings in case Darth Vader ever bit it as disappointingly as Darth Maul had done for him earlier. For that matter, Darth Tyrannus/Count Dooku could very well have been devious enough to secretly be setting up his bid to get rid of Palpatine and assume the role of master rather than apprentice as well, with his own "apprentice in the wings."
With all these junior level not quite Sith guys that it makes perfect sense to have waiting in the wings, it's not hard to imagine one of them stepping up his efforts and becoming a power to rival Luke Skywalker and his fledgeling Jedi organization. Seeing the disastrous (for the Sith anyway) way in which Palpatine went down when Vader had his deathbed conversion back to the light, the whole rule of two thing would probably be thrown out. (This has the added bonus of allowing you to remove one of the Episode I and II isms from the game.)
Now, I know you mentioned that Amanda is not playing a Jedi character, nor is she necessarily really into the thick of Jedi-type plotlines, but as a force sensitive (who doesn't even know it yet) bounty hunter, she's in a good position to attract the attention of both the Sith and the Jedi who may want to recruit her to their respective folds.
