Why on Earth should the script be chained down to twenty years worth of novels? Believe it or not, there are casual fans who have never read them, and average moviegoers who just like the original films. Disney would like them to buy a ticket. Having to explain why Chewie's not around is going to be a distraction and a downer.

Saying the novels were canon when there weren't going to be any new movies might have made sense at the time, but it's just going to cause problems now.

Isn't there already a minor continuity issue with where the Clone Wars micro series fits in with the CGI show?

You don't have this issue with Trek. The shows and the movies are continuity king.