Gene wasn't in the best position following TMP's less than positive reception. If I recall my old Starlog articles correctly, he was asked to vacate his offices on the Paramount lot at one point. TNG was still several years in the future.
One interview he gave with Starlog in the years between TMP and TNG mentioned a pretty awful script idea, with Spock having to kill Kennedy to preserve the timeline. I'd like to think he was pulling the fandom's collective leg, but you never know.
Gene's "tenets" applied to the 24th century. I don't think it was ever a denial of way things were in the TOS era. Having a Klingon on the bridge was his idea too?
For better or worse, Rick Berman was hired by Roddenberry.