I can understand wanting to protect franchise the franchise, but it seems to me that the issues came about when his ideas of what the franchise are/were conflicted with other peoples ideas.
Isn't that the only time "issues" are raised? The writers were employed to write good stories, Richard read the manuscripts to make sure they fitted with GR's ideals and didn't clash with canonical facts, and Paramount/Viacom read the manuscripts to ensure the reflected the paramters of the licensing deal. Somewhere in there, issues will
be raised, no matter who's doing the jobs.
I know that one of the first things to niggle at Roddenberry was fans demanding to know why the movies weren't acknowledging enough/all concepts proposed by Franz Joseph in the "ST Technical Manual" and bridge blueprints. Joseph's licensing contract had permitted him to sub-license his designs to "Star Fleet Battles", which was way too warlike for GR's tastes, but there was no loophole in the contract to stop the stuff coming out, or insist that it be modified, although it did undergo some changes in the game's next incarnation.
Another early sticking point was a convention distributing fliers that proclaimed GoH novelist Diane Duane as "the creator of the Rihannsu". Diane Duane had no idea she'd be promoted that way, and only 2% of the viewing audience read the books anyway, but part of Roddenberry's and Paramount's roles was to ensure that the franchise remained recognizable (and the TV series and movies had only ever called the Romulans "Romulans", despite how logical and clever Duane's novels were).
And then came TNG, which coincided with the winding down of Filmation and
a groundswell of new licenses, so a 1989 memo reclarified "what was canon", resulting in the removal of TAS elements from the list of things that could be used in other licensed tie-ins.