With the Marvel comics, they were released prior to Empire Strikes Back and before there was a concerted effort by Lucas Licensing to maintain a consistent continuity. Moreover, any inaccuracies regarding Vader, Kenobi and the Skywalker clan were a result of Lucas changing his mind as all story elements pertaining to them had to come from the man himself.
The only big change is Boba Fett's origins; which is again because Lucas changed his mind. Originally, he wasn't meant to play any part of the prequel trilogy (hence, why EU writers were allowed to write about his back story) but when it came time to develop the prequels, Lucas decided to include him anyway.
So basically he decided that it was his story and that even though he let other people add to it, he still had the final say, just like I have been saying.
Only insofar as they were hired to do a job. It's not like they went to LucasBooks with completed manuscripts seeking publication. Rather, it's the other way around; with LucasBooks hiring them to write novels for the Star Wars franchise.
Also, something to consider is that when Disney bought Lucasfilm, a portion of that money was to acquire the intellectual property of the various books and assorted merchandise associated with the EU that Lucasfilm, and its various subsidiaries, had published. Meaning, to rendering it non-canon devalues said intellectual property; essentially burning the money they had spent acquiring said property in the first place.
Even if this is calculated as an acceptable loss, Disney would likely want/seek to pull the existing copies off the shelf as they would be actively harmful to the franchise. The Star Wars EU is unique in that they are all for the most part in continuity and connected to one another; unlike most other EUs which consist mostly of separate, standalone books. If this continuity is not consistent with that of the new movies, it will confuse new fans who are unfamiliar with the existing EU franchise prior to the new trilogy. Worse, if continued to be available, it could discourage the new fans from buying subsequent EU merchandise that's based on the new trilogy (as they wouldn't know which individual books to buy).
In short: Rendering the current EU franchise non-canon would cost Disney money; both, by diminishing the value of Disney's intellectual property and discouraging consumers from buying the new trilogy's associated merchandise.
You're giving the EU WAY more value than it has. It's not going to derail the Star Wars franchize. Star Wars makes a majority of it's money from Toy Sales. The Comics and what not are a factor too, but a small one compared to the merchandising. Not to mention, these novels and comics are not as big as you seem to think they are. The average casual Star Wars fan, doesn't run to the book store to buy Star Wars EU books, after viewing the movies. With the internet a lot of Casual fans know small facts here and there about the EU, but the majority don't closely follow.
It's like how casual fans of the Spider-Man films or the Nolan Batman films don't all read comics or are familiar with the Marvel/DC mythos at all. Do you know how many people were in my midnight screening of the Avengers talking about how they wondered why Batman wasn't in the film, or that thought Thanos was Hellboy?
Disney most likely will not pull the EU from the shelves, rather they will simply label them into a different continuity.
