I think the op has a good point; this represents a significant "lost opportunity" for Bioware. You are allowed to do terrible things, yes, but where are the consequences? In fact, one of my main beefs with the Class Stories is there are very few consequences to the player's decisions. I currently have a 50 BH (light side), a 46 JK (Dark Side), and a 47 IA (mix, mostly light), and I've been comparing notes with guildmates on where our respective class stories leave us. It seems to me that, other than a few in-game mails from NPC's, our widely divergent moral outlooks and decision making led to the exact same circumstances. This is where TOR differs from ME 1/2 and other Bioware classics. In ME, you are allowed to make these widely divergent decisions, but there are real consequences for those actions. Good storytelling explores both the act and the result, and in a lot of ways TOR's class stories are indifferent to your character's decisions. Much of this is necessitated by it being a MMO; mechanistic concerns trump story every time, even in TOR.
That being said, some class stories were written better than others. The IA story was an excellent one, with believable light/dark options at most stages. It really tried to explore the story of a "regular guy" dealing with an Empire run by Sith.
I guess I just wish there were more consequences...I wish my Jedi could get expelled from the order, I wish potential companion death/loss was there to remind us in some small way that those decisions matter.