Was Jim Kirk's mother shown to be Starfleet, or merely aboard a starship?
In "Conscience of the King", we could just as well decide that young Kirk's parents were killed by Kodos, too (or at least one of them was), and this made Kirk join Starfleet. He just maintains his cool better than Riley, which is sort of a story point anyway. This decision wouldn't be contradicted even by STXI, which only describes events 14 years before the TOS episode and then alters the timeline. The death of Kirk's custodian(s) would have explained why this person does not (these people do not) qualify as eyewitness(es) to the massacre.
Incidentally, the calamity mentioned in the episode, a contaminated food reserve leading to famine, doesn't make much logical sense unless we make certain assumptions about the nature of the colony. 8,000 people could never have starved to death if they lost their food stores on an otherwise habitable planet; the only way the loss could lead to a famine would be if the planet was largely uninhabitable, with the colony perhaps built underground, or under protective domes, or something.
This is a bit more high tech than most of the colonies seen in Star Trek. Quite possibly such a colony would have needed technological help and advisors, thereby involving George Kirk Sr. from Starfleet for some length of time. He would then have brought along his family...
If Kirk's custodians weren't killed by Kodos, then we have to explain how they can't be eyewitnesses. Perhaps they died later on? But the computer claims that there were only nine eyewitnesses to begin with, and several of them are dead already by the time of the episode. So apparently most of the 4,000 survivors didn't bear witness to Kodos somehow; Kirk's parents could have been among those.
How come 3,991 people could have missed seeing the face of their governor? Well, Kodos obliquely refers to a coup that may have brought him to unlawful power, ousting the real governor. And "Kodos" sounds like a false name anyway. Perhaps the person who became Kodos rose from the ranks of obscurity while wearing a ski mask, and only these nine people ever saw him without his mask?
Still doesn't wash very well, though - because Starfleet archives contain a photo of Kodos!
So perhaps everybody saw the face, but only those nine people knew who this person had previously been? Perhaps "Kodos" arrived on the same ship as Kirk, Riley and their Starfleet parents, saw a colony ripe for picking, and organized a coup there - killing 4,000 colonists and all but nine of the people who knew who he had been (or who he had pretended to be, since he probably always went under aliases, being a villain through and through) during the trip there?
The latter option would still be in line with everything we know of Kirk, including STXI.
Timo Saloniemi