AFAIK the EU books have always been considered as non-CANON. And rightfully so, because in a lot of cases, they don't pay much attention to the necessary details. There are numerous moments where the books contradict the films, or things in other books. Though there's an official "Holocron" of CANON information that authors have access to, still a lot of things slip through, and I don't think there's anyone at Lucas who reads through these books before publication to make sure everything is as it should be.
As for a fan rebellion... I think the odds of that are pretty slim. I always thought Star Trek fans were even more vigilant than Star Wars ones, and the Abrams film didn't take nearly as much flak as I expected it to. Seems most just complain about the lens flares rather than the plot, or the way it seems to defaecate on the source material. Same is true for Star Wars Episode 1. Very few complain about the overall story. They just don't like how the film was made, and would prefer that Jar Jar and Jake Lloyd could somehow be erased from collective memory.