I know I'm rezzing an old thread, but I'd just like to say that "playing the good guys" is the leading reason I haven't picked up any of FFG's rpgs. The black and white dichotomy in the canon SW universe is too restrictive. Give me gray jedi and teetering Sith. The SW setting needs more moral ambiguity, and I'm hoping to see some of it leak into the new movies. Well-intentioned but mislead Stormtroopers isn't only the more compelling story; it's the one people in the US and Europe should best relate to.
Dark-side force-users get minor penalties (certain number of destiny points auto-flipped to dark side, and hit to strain threshold), but also get certain boosts (dark side points - which are more frequent than light side - become the main fuel for force points, and they get wound threshold boosts). And you can also have FaD characters that don't deal with Morality (this requires them to take Duty/Obligation instead though), thus leaving them perma-grey mechanically (though narratively you can switch them to dark side if you feel it's necessary).
Besides that, there's literally no reason you can't be the bad guy. You can be an evil Rebel who goes to far, a good guy Stormtrooper, or a smuggler that sells spice to kids. Just because the intention of the books is made for what most people are going to be - generally good people, doesn't mean you're stonewalled from doing what you like.