So much of the implementation of Order 66 and the Great Jedi Purge happened offscreen when we weren't looking that there's still plenty of room for individual writers' interpretation of the events surrounding Palpatine's creation of the Empire. According to written reference materials there were roughly 10,000 Jedi Masters, Knights, Padawans and child inductees in the Order during the time period of the Prequels and the Clone Wars and we saw how many killed off in Episode III, counting all the dead bodies strewn around inside the Jedi Temple: a few dozen or so? That leaves thousands of other stories to tell, and the Purge didn't all happen at once. Some Jedi didn't perish until Vader and his new Imperial Stormtroopers hunted them down later on.
I don't think there's really much one can screw up when it comes to Order 66 because we saw relatively little of it and it wasn't a quick, overnight operation to begin with. Let new writers tackle it if they want. Short of some dumb new reveal that Order 66 didn't in fact originate with the Sith and the Kamino cloners there really isn't anything they can do to screw up the continuity of the Purge. Besides, the EU will be discarded at will from this point on if it doesn't fit in with new animated or live-action, filmed productions.