When it comes to Kirk's love life, we need to remember the limitations imposed on old-time movies and TV when it came to actually showing or stating outright that two characters have sex.
Many Star Trek plots simply don't have time in them for anything to follow the discussions/kisses that we see onscreen. "Mirror Mirror" is a great example because not only do the two characters have to stop what they intend to do to deal with the tech problem of the episode, but also because Marlena actually explicitly complains that nothing more went on between her and Kirk at that moment. Some other episodes, though, do have plots that do allow time for things to happen off-screen.
I do see where you and others are coming from about "implying" being done in old shows, but that really only fits in a handful of Star Trek cases without altering the plot. I do not think anyone is really suggesting the audience is supposed to infer that the actual events of the story are directly different from what is seen onscreen. Would we be, for example, supposed to assume that "more" went on between Kirk and Marlena, even though that is directly contradicted by the pacing of the plot?
If the answer were yes, then defining a Star Trek "canon" would be impossible. Any onscreen moment, of any nature, could be inferred to be different than what is shown, based on what we think was "implied." Although there is no real reason any single viewer could not to view the show this way, if one is seeking to create a consistent storyline across many episodes you have to start somewhere, and taking what's onscreen as "what actually happened in-universe" is about the best one can do to get consistency. If not, then modern visual storytelling getting more and more "explicit" just fuels any current show-runners' claim that "Our version is the most correct!"
Now that I think about it, this phenomenon I just described may well explain the "character drift" of the original poster. To name a few: Kirk's life, the level of tech used on the Enterprise, Starfleet's policy--all would look very different, depending on if your lens is what was actually shown onscreen during TOS, or if your lens is, "An old show could not spell it out--here's what REALLY happened!"
Nobody is mining The Alternative Factor for series defining continuity either.
This is an interesting choice of episode for your example, given that this is one of the episodes I have mentioned as having scenes that may have implied Uhura is in command, but just not actually shown it.
A remote toxic relationship interspersed with in-person time together. She wouldn't have wanted to kill him (likely) if they had stayed together, undivided by her inability to work things out, her womanhood, and everything else she thinks stands in their way.
