In the cancelled Kenner toyline called Star Wars: the Epic Continues, the main villain was Atha Prime, an architect of the Clone Wars who exiled by the Emperor. You could say Atha Prime rebelled against the Republic, who were trying to seize his cloning tech and/or he attacked worlds using clone armies. Just a thought.
BTW, nice job DuracellEnergizer for using the concept in your PT rewrite. I really notice it until I saw the article on Atha Prime.