If you defect to the SIS at the end of the Agent storyline, Do you properly defect and work for the republic? Or does ardun just tell you "You'll be a double agent again, but for US this time!" And then he has you work for the empire? Because that sounds utterly disappointing.

For the moment, that's all there is. You become a double agent working really for the Republic but inside the Empire. It's possible that the post-Onslaught story there will be a universal way to defect (it's not clear whether they will, but it is nevertheless hinted at in some of the material), rather than having it be just the IA that can do it or having some method shoe-horned into a story that doesn't suit it for the other classes.

 

Think of it this way: how would you fit a defection into the other stories? Bounty Hunter and Smuggler don't seem *too* hard, and the Trooper could pull mission like the one on Arron Prime, but the Jedi and Sith stories don't seem well-suited to it.