That's the trouble with verbal orders; they are interpreted by the giver and receiver in ways not necessarily in accord with what was said at the time.
I realize this is too serious a subject to compare with a movie, but a scene from "Rio Grande" with John Wayne, is on topic. J. Carroll Naish, playing Gen. Sheridan, orders Wayne, as Captain kirby York, approaching retirement, to cross the Rio Grande into Mexico in pursuit of the hostile Indians then on the warpath. He tells York that if he is caught, Sheridan will deny having given him such orders, but that he will hand pick the members of the court martial.
Gen. Heth colored his remarks to Keith, so that what he said was said could not be interpreted as orders to "take no prisoners" to the extent captured combatents could be executed, and that certainly women and children were not to be harmed. Although not clear from the correspondence posted on the subject, I suspect everone but Governor Vance just wanted this matter to go away. Keith's resignation would have the result of removing him from Army control, and putting the ball in civilian hands. I am not aware that anything was ever done to punish Keith. Stan