Wholly sidestepping writer intent, which never amounted to much and never was intended or required to, we should look at what was actually said, and decide how to best mutilate that to provide a logical conclusion.
The "eyewitness" issue is by far the easiest shot to take there. Let's review pertinent statements:
"There were only eight or nine of us who actually saw Kodos."
"Burned body found when Earth forces arrived. No positive identification."
"Kodos: file of all survivors. There are nine actual eyewitnesses who can identify Kodos."
So the nine are survivors, and stand out by virtue of being able to identify Kodos.
Does this mean there are other eyewitnesses who are unable to identify Kodos? Any survivors would naturally come in two sorts: those who survived by being elsewhere when bad things happened, and those who survived despite being right there. The latter sort could be eyewitnesses to the massacre, and relevant to court proceedings; the former would be irrelevant bystanders.
So, does being eyewitness (in general, or in being one of the nine) mean being able to tell what Kodos looked like? But that's nonsense - there are pictures of what Kodos looked like, and the human eye can do no better than pictures (and will generally do much, much worse). The nine need to be a more knowledgeable bunch, with access to more than the fallible input of their eyes. And it's simple for them to be that: they could be the nine who know who Kodos
was.
There was a "coup" on the colony. So "Governor Kodos" could be a coupster whose nom de guerre tells the authorities nothing and whose real, original identity is uncertain. But nine people who traveled to the colony on the same ship with the mystery man who then became Kodos would be valuable sources of information indeed, when the time came to "identify Kodos". There would be records on the passengers of the putative ship, but then there would be these actual eyewitnesses...
(In this model, the "no positive identification" bit would be the computer saying that nobody could positively, that is, absolutely, ever identify who this Kodos guy was, which is a premise acceptable to today's audiences, and not that the authorities couldn't positively say the corpse was Kodos, which is an unacceptable premise.)
Now, the other alternative is that of the eyewitnesses establishing Kodos' specific guilt on giving the illegal and murderous orders. But this is
not what gets established in the dialogue. Nowhere in the episode is eyewitnessing associated with the ability to prove that the massacres happened (there's no shortage of proof that they did take place, AFAWK), or with the ability to prove that Kodos did it (he freely admits to this in a public speech!). Furthermore, the computer is aware of the eyewitnesses being eyewitnesses - so eliminating them now, decades later, would serve little purpose as regards the above two points, on which they either must have been questioned, or then flagged as valid providers of incrimination on demand, therefore as good as having already provided that incrimination!
OTOH, if the nine and the mystery man
were shipmates, then it would be plausible for the nine not to volunteer information initially, lest they incriminate a friend or a family member - perhaps Kodos was somebody trusted or recommended by Kirk's dad, say? True or not, Lenore might suspect the nine of holding back key knowledge that would connect the pasts of the two fictional identities Kodos and Karidian and lead the authorities to the true identity of the man behind both.
That the testimonies of the nine would be necessary to get Kodos convicted doesn't sound plausible, as Kirk doesn't think this would be an option: instead, he makes a personal threat on Karidian's life, something rather unthinkable if an official alternative existed, and then fails to pursue that, again unthinkable if there were official obligations. If the fate of Kodos hangs on Kirk's testimony, these facts make no sense be Kirk vindictive (he'd then give the testimony and let Kodos hang) or merciful/afraid/protective (he'd then not make death threats). And it certainly makes no sense for Kirk
not to dictate an official witness statement ASAP, totally preempting the murderer's efforts!
If, OTOH, the testimony is irrelevant as regards the sentence of Kodos, and only matters in whether Karidian can be established to be Kodos, then Kirk is correct not to jump to conclusions; Lenore is correct to be protective of her father's new identity and secret past; and the death threat is understandable if we make the additional assumption that the sentence already passed on Kodos (or awaiting him if it is discovered he's alive and pretending to be Karidian) is one of letting him walk. The conclusion of the episode establishes that murderous madmen (madwomen) do walk, to the mental asylum and back, and Kirk might not be comfortable with that newfangled thing yet, although he'll learn better by the time of "Dagger of the Mind".
But never mind these thousand-word treatises. Ultimately, this episode isn't particularly problematic as long as no writer makes a misguided effort to "explain" or "excuse" it. The whole Kodos thing is a McGuffin and openly treated as such - it doesn't seem to matter to our heroes, who don't make even a halfhearted attempt at "unraveling the mystery of the identity" or "making the villain face justice", even when at least Kirk obviously feels strongly about it all. As per the rules of the episode, the crimes of Kodos either cannot be nailed on Karidian no matter what, or won't carry a consequence worth all the hassle - and it takes a deranged mind to think otherwise. In the end, even Karidian himself appears to concur, condemning his daughter's efforts as utterly counterproductive...
Timo Saloniemi