Having maxed an Inquistor in Beta all lightside, the choices aren't as great in the main story as you would have liked it to be. However with the Sith Warrior (lvl40) I've noticed it seems they went out of their way to make it more pivotal. As in, it's recognized in the class story midway through what type of alignment you are...also the padawan you pick up is able to detect your alignment and makes a comment about how pure you really are...Never had that sort of thing happen at all for the SI, it went pretty unnoticed.

I will saw though that being a Light Side Sith is a more pragmatic realistic way of trying to be good...whereas Jedi's are probably too idealistic.