What Nimoy wanted in 1988-1989 weighed more than Fontana's memos on a different production in 1967-1968.
Also, there's a difference between a show staffer's guidelines for freelancers and what the people in charge of the show (or film series) are free to do. Generally "don't do this" guidelines are meant to deter freelancers or pitchers from offering up the umpteenth iteration of an overused trope and encourage them to come up with fresher ideas. But that doesn't mean the makers of the show will forbid themselves from using the trope if they have a good reason for it. For instance, when I was scheduled to pitch for Voyager's third season, the letter from Jeri Taylor that came with the pitch packet advised pitchers to avoid time travel ideas because they were already "overbooked" on those, probably referring to "Future's End" (and then we got "Before and After" later in the season). She also said they wanted to get away from stories about the quest for home and focus on just exploring the Delta Quadrant, but then they went and did "Scorpion" at the end of the season, completely reversing that policy.
A guideline in TOS against giving characters hitherto-unmentioned relatives seems like the same kind of thing, since that's low-hanging fruit as TV plots go. But it was most likely just to discourage freelancers from overusing the trope, not to prevent themselves from doing it, since Fontana herself gave us "Journey to Babel." No competent TV producer or story editor is ever going to impose an absolute ban against using an idea, because you never know when someone might come along with a really good, fresh approach to that idea. It's just to keep themselves from getting buried in the same obvious and cliched pitches over and over.