Oh, they could very well have made Rex decide to go against Republic orders and go rogue. Especially after Rex finds out that he has an overwrite switch that he never wants to hear the code word for. But the most probably version would have been that while there's conditioning, "love" or brains can overcome it, so people like Rex and Fives can fight against the conditioning. See, all of this is guesswork which will likely be over by the time the DVDs are released, but I don't get the feeling that they are planning for a strictly Republic Handbook of Assorted Orders explanation. And they won't go out of their way to keep the Traviss interpretation in, especially not if Lucas' version is fundamentally different. TCW was Lucas-influenced enough that they actually tried to show and explain a few things which had so much freedom for interpretation in the movies that EU naturally tried to find their own explanation. As for the Sifo-Dyas bit not making sense: It never made sense to introduce an offscreen Jedi and give him offscreen incentive and offscreen money to build the clone army. It made all kind of sense for Sidious to order it himself and give it to the Jedi, maybe even under a comparatively elaborate plot construction in which the Jedi think that they snatched the army away from the evil guy, and that the evil guy only played Jedi because the Kaminoans wouldn't have build an army for anyone except the most noble people in the universe. Now, we have amoral Kaminoans who only look at the size of your pocketbook and Yoda who fetches an army because, well, you know, because. Giving explanations like Palpatine playing Plagueis playing Sifo-Dyas giving blood for Grievous does work, of course, but I don't think it's a smooth solution to a problem that was extremely non-smooth.