I am quite aware of the holocron and the Karen Travis saga. IMO, part of Lucas showing he really couldn't tell a story anymore was his desire to have a warrior race taken over by pacifists.
That aside, the book isn't written based on the final cut of the film. It just can't be considering it is released the same day as the movie. That includes the audio version of the book. Let us assume that Rey and Kylo are brother and sister in the original draft of the script. It doesn't get revealed in the to the viewer directly, but is hinted at with the "it is you" line. This first draft script is given to Alan Dean Foster which he uses to write the novel. The novel gets approved by Lucasfilm/Disney. After that time, new script drafts are written, changes are made, etc. By this time it could be easily too late to change the final edit of the novel. There are things like the Snowspeeder chase and Chewie ripping off Plut's arm in the novel that we have now seen as deleted scenes. That does not mean they are canon. The "it is you" line is only canon if Leland Chee or Pablo Hidalgo or someone else from the storybook group confirms that it is. As of now, it contradicts what is seen in the theatrical release, which would seem it is not canon based on the previous statement from the story group.
Both the TFA novel and the Rogue One novel are closer to the final product than the OT and PT novels, but they are still differences which most likely comes from script edits and final cuts of the film.