I've seen this point made a few times in the past, and made it myself once or twice, but it's a good one. Thompson's death proves that ''the black guy always dies first'' is slightly exaggerated. In fact, Ensign Watkins, Scotty's assistant in THAT WHICH SURVIVES, is the only black crewman of either sex to die in classic TREK's TV episodes. He's also the last crewmember to die on the show if we go by stardates or episode production order.
There's a slight possibility had Lt. Shea been white, he might have been killed in typical security-guard fashion. But this way is less predictable storytelling and works better. At least Thompson wasn't sentient at the time. I hope.
Part of the problem is, she's never mentioned after the beginning of Act Two, which contributes to the disposable nature of so many redshirt characters. All the other crewwomen who died were blueshirts, unless you count Marla McGivers after the series ended....
Theoretically Rojan could stand trial for the execution, but since Kirk and company needed to make peace with the Kelvans, it was apparently swept under the rug. Putting him on trial might not sit well with now-friendly Kelvans.
The episode for those reasons begs for a sequel. As it turns out two or three writers have made stories on the web involving Yeoman Thompson's death. The shortest and probably best of them is ''No Apologies'', which can be accessed by googling ''Death of Yeoman Thompson, Star Trek.'' To summarize:
Rojan and the Kelvans are applying to colonize their last planet and make peace with the Federation. Two things stand in their way: Yeoman Thompson's parents. Both are scientists and doctors, and have seen their share of the deceased. They tell Kirk and Rojan that they won't stand in the Kelvans' way, providing their daughter is restored to human form. Rojan explains that wouldn't be pleasant, but the father insists. Rojan reluctantly complies, what's left of Thompson is restored, and the now-humanized Kelvans freak out at what Rojan did. Kelinda gets sick, and Hanar decks Rojan, shouting at her ''She was beautiful!'' Kirk phasers the Yeoman's remains at her father's request. Then the father tosses Rojan out of his house, but won't deny him Federation membership.
Now THAT's a suitable ending in my opinion. It smells like..... victory.