I think you misunderstand the definition of "countermanding" If an order is countermanded, that means that either the person issuing an order, or a superior officer has canceled or taken back an order that they had given, which is within their right and no punitive action would be necessary.
- Orders are countermanded by superior officers, and (in limited, justified circumstances) belayed by subordinate officers. Although, "belay that order" may occasionally be used as a misnomer by a superior officer over a subordinate one, since although the legal authority from which such an order is given is different, the outcome is the same, that of one officer overruling another. ---ProfessorTrek 10:54, February 13, 2012 (UTC)
do you mean disobeying orders? Although no regulation has been stated on screen to the effect, it would probably warrant serious brig time as well as a court martial. Serious cases could be considered mutiny, which is a very serious crime. Usually if a court martial is involved, the attending judge would decide an appropriate punishment. It should be noted that in modern military courts, either disobeying a superior officer or mutiny can warrant punishments ranging from brig time or dishonorable discharge to the death penalty. However, it is stated in TOS that by that time there is only 2 death penalty worthy crimes left on the books, violating general orders 4 & 7. It is not known whether or not the death penalty is still on the books in Archer's time