You're basically asking for a whole new game, where the companions have different interactions or you have all new companions, the players have all new dialogue and interaction with opposing faction npcs, and where the stories end entirely differently or the endings become meaninglless and need to be replaced by new endings. And all this for a fairly small percentage of characters who would change sides. It's not feasible.
Would be nice for a single player RPG though. Not in the half-***** form we see it in most Star Wars games, but in a way that the story is totally different if you defect to the other side.