It isn't as cut and try as Jedi=Good and Sith=Evil.. Take Mace Windu for example, one of the more important Jedi in the films and holds a seat on the Jedi council. Mace Windu was willing to kill the emperor in cold blood for the greater good even though he was aware it wasn't what he should be doing, this would have gained him dark point in SW:TOR. Sometimes bad stuff has to be done to get a good outcome.