It's a pretty safe bet that it's never gonna happen simply because your faction and story/companions are too deeply interconnected and they'd pretty much have to create a second layer of story on top of all the existing stuff just to accommodate it.
That's not to say that they'd never do it, but it would be a massive undertaking for them and, as such, likely falls outside of their current plans for the game.
They'd not only have to create the story for your "defection" but also any future storyline content ( if there ever is any ) will not only have to be created for Republic and Sith, but also additional storylines for defectors of both sides. It would double the work already required.
EAware screwed themselves when they made the game story and voiceover dependent, because it is the single biggest obstacle to keeping new content flowing and makes even the simplest additions ( such as defection ) a much more expensive and time consuming chore than it would be in any other game.
For example, when will the guy or gal who voices your character be available? Will they be available at all? Do they even want the job any more even if they are available? Now what about the people for all the other player character and NPC voices? Will they all be available within a certain time frame, or will you have to draw the development time out to compensate ( prolonging the time it takes to get your content released and increasing costs )?