Based on the quotes I linked to above and the TMP novelization forward, GR was of the opinion that the Klingons always looked like they did in TMP, season 3 and TAS never happened and neither did the "foolishly heroic" parts of seasons 1 and 2. Roddenberry was nothing if not a revisionist.
Here's the relevant section...
Unfortunately, Starfleet's enthusiasm affected even those who chronicled our adventures, and we were painted somewhat larger than life, especially myself.
Eventually, I found that I had been fictionalized into some sort of "modern Ulysses" and it has been painful to see my command decisions of those years so widely applauded, whereas the plain facts are that ninety-four of our crew met violent deaths during those years - and many of them would still be alive if I had acted either more quickly or more wisely. Nor have I been as foolishly courageous as depicted. I have never happily invited injury; I have disliked in the extreme every duty circumstance which has required me to risk my life. But there appears to be something in the nature of depicters of popular events which leads them into the habit of exaggeration. As a result, I have become determined that if I ever again found myself involved in an affair attracting public attention, I would insist that some way be found to tell the story more accurately.
(P. 7-8)
This isn't one or two incidents he's denouncing, but the entire depiction of the 5-year mission. Roddenberry is saying "forget that, this is real Star Trek."