^I'm not sure why you'd class those characters as Mary Sues. Remember: It wasn't unusual in '60s or '70s television to build an episode around a featured guest star, so just having someone come in and be the focus of attention for one installment doesn't make them a Mary Sue. A Mary Sue is a character who steals the spotlight without deserving
to -- a character, usually a wish-fulfillment surrogate for the author, who is described as being a totally awesome and wonderful person who upstages and is adored by all the main characters, yet who has no actual qualities making them worthy of such admiration either by the characters or by the readers. Bonus Mary Sue points if the main characters all end up acting totally out of character in response to the featured guest. Schaeffer was a textbook Mary Sue in every respect -- she was this incredibly admired class of super-agent that had never been mentioned before, everyone fell in love with her and acted out of character, and she was supposed to be the toughest, smartest woman around, yet she melted when Kirk flirted with her in condescending baby talk that would've gotten him a trip to sickbay if she'd actually been the tough, liberated woman she was alleged to be.
I guess I can kind of see how Flynn and Hunter would qualify. Flynn was a new character added to the main cast and given an important role as a member of the group, and Hunter did kind of fit the "more awesome than the heroes" model. But they were both reasonably well-drawn characters who were actually interesting and worthwhile. And honestly, given that the TOS cast was overwhelmingly male, it's not surprising that so many authors in the '70s and '80s would try to balance that somewhat by adding a new prominent woman (and Phase II
intended to do the same by adding Ilia, by the way). As long as the character in question is actually engaging, I don't have a problem with it.
As for Jean Czerny, I don't remember that book too well, but I don't see it. As I recall, she engaged mainly with Kang, and served as a viewpoint character for a journey into Klingon culture. I guess she did end up being widely admired and impressive to the Klingons or some such thing, but it wouldn't have been much of a story if she hadn't caught the interest of the Klingon characters to a sufficient degree that she could get to know them and be a participant in their lives. Maybe not a Mary Sue so much as an analogue for Kevin Costner in Dances With Wolves
or Tom Cruise in The Last Samurai
-- the "one of us" who gets immersed in the exotic foreign culture and serves as our viewpoint figure in it.