it's really not as many as you think. Like less then 1% of them are diehard EU fans and we all know after the Prequels they were still huge fans.
I would really like to see where those numbers come from because so far I have no reason to believe them. If the EU didn't sell they wouldn't produce stuff to it.
eitherway, my main concern is that since a lot of the events and characters is tied together in the EU. Change one wrong thing and you might effect several storylines. for instance lets say they make the Vong wars uncanon. Well alright they were rather boring anyways. however that would effect the character development of Jacen Solo meaning no Darth Caedus = the 8 Legacy of the Force books are uncanon, ups!
The same thing would happen if they should decide to kill some key character, lets for instance say they kill of Mara Jade before she originally die at the hands of Jacen. Well, first of all Ben Skywalker might not be burn, secondly Jacen would have to sacrifice someone else to become Darth Caedus = story is uncanon.
Then if that happened the Fate of the Jedi novels would also be uncanon since they are affected by the effects in Legacy of the Force etc.
As I said one stupide move might destroy a great many storyline and THEREFORE Disney need to be careful.
However, if they manage to do that there might come much good out of them buying Lucasfilms.