I think that the deserter episode was the setup to eventually get Rex out of Order 66. I think they've made him too much of a hero now to kill him off / let him go bad. So I suspect he'll desert at some point.
It would fit because in ROTS a Commander Appo is leading the 501st. So either Rex dies or he deserts. I like though how they kind of followed the RC/IC books by showing how some Clones know it's not right, but they still feel obligated to their job and the other troopers because that's all they know.