Q: Can a good Sith or bad Jedi change sides? Faction changes?
A: No. Interesting story... originally there was a third underworld faction (Wall of Crazy)! It becomes very expensive from a development point of view if we'd have to double the number of stories. However we are always looking for ways to figure that out in the future. You never know.
Now, let's just imagine that for a second before we let reality crush our fantasies once again.
Is BioWare saying "you never know" an actual "you never know" or a "that's never fucking happening"?
I think allowing faction-switching would be fantastic for story and roleplaying reasons, but godawful for the whole MMO part of it. Imagine if you lost half your guild because they suddenly decided they wanted to be Sith. Imagine PvP balance if the underdogs decided they'd rather be part of the zerg on the other side.
Cute idea on paper, probably a nightmare in practice.
The 3rd Faction is not ever going to happen. (Not enough time, resources or Force users to go around.) If you want 3-faction RvR (and you should), you will have to actually hope that Prime and TSW aren't garbage. Because you won't ever see it happen in SWTOR. No matter how much we all know that the game needs one.