Change the rule of canon = onscreen Trek because it never envisaged a TV / film split fiasco, which is what this looks to be.
That's not a rule, it's just what the word means. People have this strange idea that "canon" is some official seal of approval. But it's really just a descriptive term applied by fans and critics to refer to the original work itself as distinct from derivative works like tie-ins or fan fiction. The label does not make the thing what it is, it's merely a shorthand way of describing what it is. Calling something land doesn't make it land, it just describes the fact that it's different from water. You can't change the "rule" defining what land is so that it includes water, or so that it doesn't include deserts.
Anyway, how canon is defined has nothing to do with how tie-in licenses work. It's just the nature of the beast that some licensees don't have the right to use every aspect of an original work. That's not unique to the current situation with Pocket and Bad Robot. When Marvel Comics got the license to do comics based on
Star Trek: The Motion Picture, they didn't have the right to elements from the original series, so they had to avoid doing sequels to TOS episodes or bringing back TOS characters (although they managed to sneak several characters and a number of concepts from TOS under the radar nonetheless). There's a series of unofficial
Doctor Who tie-in novels about the character of Alistair Lethbridge-Stewart, licensed by the creators of the character rather than by the BBC (because in the UK, individual TV writers retain the rights to their creations), and originally they were only able to tell stories about him as a colonel because his promotion to brigadier wasn't written by his creators -- although they've since gotten a broader license and have been able to broaden the material they can cover. Similarly, the Australian
K9 series has the rights to the K9 character courtesy of his creator, but not to any other elements of the
Doctor Who mythos (including K9's design), so they had to redesign him and give him amnesia about his life with the Doctor. Then there's
RoboCop: The Series from the '90s, which weirdly had the right to the RoboCop/Alex Murphy character and the basic situation and setting, but not the right to any of the supporting characters, so all the other characters had to be either replaced with surrogates or renamed.