I guess the whole dark-light side choice thing is to give you a chance to take your character where your (his/her's) heart desires despite the represented side of the war.
My Jedi is not evil... or at least he doesn't think he's evil. Yes he's consumed by the Dark Side, but he believes to be doing the right thing. He doesn't try to do the right thing - he just does it... as far as he believes. Yes he might be brutal at times, but ultimately he sees his choices as necessary sacrifices for the greater good. And he hates the Empire with his entire soul... word "hate" being the key here