Three thoughts:
1. What is canon? For example the Jedi forms (Shi-Cho, Niman etc) aren't mentioned by names in the films, CGI TV series or new books, but clearly some Force users are using these techniques in the aforementioned media. It seems pedantic to disregard them. Disney themselves have said there are levels of canon, it's not black and white.
2. There is so much stuff in The Clone Wars, Rebels, and the new books that I think very little would need to be removed from the FFG series to "canonise" it. For example I think most of the planets in the FFG books are mentioned in canon sources.
3. I would argue having a fun game is more important than worrying about canoninity.