Kirk probably gets to decide what gets reported. And he has to come up with an explanation for why the rhyetalyn shipment was almost fatally delayed. Does he want to make McCoy or Spock look bad, by going with some variant of the "contaminated batch" lie? Or Scotty, with some kind of "engine trouble" story? Does he indicate a different planet as his source of rhyetalyn, falsifying navigation data to support that story?
Or does he neglect to mention the outbreak of the disease aboard altogether?