Not to discredit what he did because he was probably one of the biggest impact decisions taken ever, he is definitely a great man and he deserves every ounce of credit, but he did not defy orders. They received no orders whatsoever, and the captain just assumed a war had broken out. They were too deep to receive orders at all. He refused to give his permission which was “legally” (military law-wise?) needed to launch the nukes. From your own link (also he wasn’t a commander at the time):

Unlike other Soviet submarines armed with the “special weapon”, where only the captain and the political officer were required to authorize a nuclear launch, three officers on board the B-59 were required to authorize the launch because Arkhipov was also the chief of staff of the brigade (not the commander as is often incorrectly reported, who was in fact Captain First Rank Vasili Naumovich Agafonov).[11][12] The three men were Captain Savitsky, Political Officer Ivan Semyonovich Maslennikov, and Executive Officer Arkhipov. An argument broke out among the three of them, with only Arkhipov against the launch.

So it doesn’t really apply. It is more one of 3 commanding officers that had a big disagreement and one of them refused to let the others give the order.