I wasn't necessarily saying you'd switch from sith to jedi or from Bounty Hunter to Trooper... I tried to keep class names and "sith" or "jedi" out of it to keep from all confusion.
Ultimately, I was just speaking... as a Republic making dark decisions to the point in which you become an Empire faction or light decissions to become of Republic faction.
I guess even as a kid I always related it all to good (Light) vs evil (Dark). Republic as Light side and Empire as Dark side. Even in the movies 1-3 Anikin went from light to dark and was no longer republic in the end.... right? wasn't Anikin Darth Vader?! lol maybe i really just don't know my Star Wars.
I also was adding that as a reward for sticking to your factions good/bad side, which clearly there is not a determined good/bad for either faction, you could have gear related.... suppose to make it even they could provide gear for either choice you do, but limit you from doing previous quests of the other faction as a sort of once you go to the other side you don't come back.