First off, JJ's approve wouldn't "make Them canon" since the longstanding rule with Trek has always been that only what airs is canon.
What you're overlooking, though, is that someone has to make that rule. And it can be changed. There are cases in other franchises of creator-overseen tie-ins being regarded as canonical by those creators -- the Del Rey
Babylon 5 novels (outlined and approved by J. Michael Straczynski) and the "Season 8"
Buffy the Vampire Slayer comics ("executive produced" by Joss Whedon), for instance. As a general rule, canon is that which is created under the direct guidance of the franchise's creator, regardless of its medium. It's not about film vs. print, since after all the earlier
Buffy comics from the same publisher were non-canonical (since Whedon didn't directly oversee their creation).
So if Abrams' "Supreme Court" chose to oversee the creation of tie-ins that they chose to regard as canonical, nobody could prevent them from doing so, because they're the ones who are now
defining what canon is. Too many fans seem to think that canon is some higher law imposed on the creators by the studio or God or something, but the studio couldn't care less about canon or consistency as long as they make a profit. Canon is what the creators say it is. More fundamentally, canon is what the creators create.
Secondly, I still think following in the footsteps of the Star Wars licence and having the books all tied into one another is a huge mistake.
That has never been the case. The modern continuity among Trek books is a matter of authorial and editorial choice and preference, not a rigid mandate. There are still books that stand alone with no continuity references (such as
Troublesome Minds) and books that directly contradict the main book continuity (such as the
Crucible trilogy and the Shatnerverse). Even within the main continuity, books sometimes conflict with each other in minor details when the good of the story matters more than strict consistency (for instance, in
Unworthy, Kirsten Beyer consciously chose not to worry about maintaining consistency with
Places of Exile where the depiction of Species 8472 was concerned).
There has never been any attempt to imitate the approach of the
Star Wars novels. After all,
Star Wars is a latecomer compared to
Star Trek, both in film and in prose. The SW novels' approach is far more inflexible than that of the ST novels.
For one thing, it's a burden on the work-for-hire writers who not only have to check their work against Trek canon, but also have to make sure it doesn't conflict with any other novels in the pipeline. That's a MASSIVE amount of work for very little money, and I don't think it makes for better novels.
It's no burden, because it's something we choose to do, not something we're forced to do. Nobody told me, for instance, that I had to keep
Ex Machina consistent with other novels or use concepts from the overall continuity. I did that because I
wanted to, because I appreciated what the other authors had created and wanted to acknowledge it. We're not hired drudges here. We're fans, not only of onscreen Trek but of one another's work in the novels. We coordinate our efforts because we enjoy it.
Very few new fans who are first-time readers of Trek tie-ins would pick up a new tie-in novel if they have to read 10 other novels to actually get the full story.
Unless a book is part of a trilogy or the like, you can always get its full story within the book itself. Any ties to other books are merely bonus links, extra material that isn't critical to the central story being told. To repeat an example I commonly use, you didn't need to see the story of Pike's battle on Rigel VII to understand "The Cage." When Marvel told that story as an issue of its
Early Voyages comic, that was just a bonus, a little something extra. The full story was contained within the episode itself. So it's a fallacy to say that just because one story has connections to other stories, it means you "have to" read all the connected stories to understand what's going on.