You may be looking for The Trials Series, a Star Trek: VOY story.
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It was published in the print zine Nexus #1.
It was written in reaction to The Rack.
A reaction to "Trial" is "A Different End" (also in Nexus #1) which is a story where Kirk & Spock really are lovers, and after that trial are now safe from invasive speculations.
One interesting note is that this author contacted the authors of 'The Rack' and gotten permission to write this story, yet nowhere in the zine does it explain this; instead it simply states it is a story written as an alternative version, perhaps leaving less-experienced writers, at the time, with the idea that prior permission was not needed.
For more on this topic, see Unauthorized Sequel.
Reactions and Reviews
An alternate version of "The Rack" by J. Emily Vance in Contact #4. Kirk dies of an overdose but Spock detects it through an empathic tie and saves him. Admiral Lewis believes they are homosexual lovers and letting the relationship interfere with their judgment and is hounding them out of the service. They now decide that they will fight; Spock will face court martial. The case turns on the legality of an order that Spock disobeyed to save Kirk. They win, based on the fact that Spock had information (that Kirk was indeed alive) based on his empathic tie, which the distant admiral did not have, and was justified in taking the risk to the ship. Well written, good characterization, if a bit too much breast-beating.