I was under the impression Disney did do something similar with Star Wars and it's 'Expanded Universe' soon after Lucas sold the rights. The Expanded Universe was no longer considered canon, or at least a part of the continuity of the Star Wars stories. Though I don't think they wrote such a deliberate change into the novels and other written properties.
Having not kept up with the growth and expansion of the Star Trek novels, I am not as invested in this change as I might have been 20 years ago. I appreciated that the books often tried to tackle stories that weren't just book-length versions of a typical episode. I didn't like all of the stories or directions they took, but that's more often than not a matter of my taste.
I also find this action unnecessary (though I might enjoy the books where it played out), as it seemed pretty well understood that most, if not all Star Trek fiction books are not considered canon, except maybe the novelizations of films and the occasional television episodes. Even those would diverge from what appeared on screen as the books were typically written well in advance of broadcast/theatrical premiere and could not account for late script changes and would often go beyond what was shown on screen to fill the space required for a mass-market book.
I guess it comes down in some quarters to a question of how intermingled various entertainment forms can or should be. Maybe it's just a power move by CBS (or Disney), or maybe they think their work needs to be produced like the Marvel Cinematic Universe. For as much as Marvel seems to be an example of single integrated narratives, there are still plenty of different universes at play when you include Marvel's comic and animated properties in addition to the film and TV work.
David