The way I'm looking at it is that you'll choose your side sooner and then be able to go after the Sith, or join them. Now once you join them you can do stuff with them like destroying the jedi by going after Atris. Just a thought. Seeing as how a lot of people wanted to do that stuff and the dev's actually took some suggestions when creating the game. The Prestige classes suppot this kind of. I mean, after a short while you'll choose your prestige class (alignment pending). So, my theory is, that on one of the meetings with Sion or some other Sith Lord, he'll offer to take you in and you can fight the other two Sith Lords or you can defy the Sith. Just a theory