More research is probably needed regarding the standing orders for operation of the watercraft which Kerry commanded. Violating such orders by beaching the boat would seem to be justified only when the lives of the crew or other friendly forces justify it.
The descriptions I have read seem to indicate that a beaching took place once for the sole purpose of pursuing one enemy combatant. That would not seem to justify disobeying standing orders which are themselves designed to preserve the lives of friendly forces.
If the enemy could expect a beaching as a response to appearance of a single combatant, then they have a perfect opportunity to set-up an ambush. That is probably why the orders were that the craft should not be beached. Kerry probably deserved to be relieved of command. I see no indication that the orders were changed to reflect Kerry's superior judgement in the matter.
It was my experience that military personnel stationed in VietNam were obligated to a twelve month tour of duty. I don't see how Kerry can justify not having fulfilled that obligation.