"Pirates of Orion" leaves many questions open about the nature, actions and fate of the Huron
crew. Which is only understandable, as the cartoon cannot show the pirates doing the logical thing and slaughtering the poor folks; the camera looks away during the actual encounter with the raiders. All we know is that skipper O'Shea survived against odds (apparently he was mistaken for dead, but McCoy was a better judge of that than the Orions), and wasn't able to tell who the attackers were but did provide data and imagery on what their ship looked like.
It could well be that these people are aboard exactly because Starfleet believes that only wetware should have the authority to fire weapons, and any ship hauling expensive items such as weapons-grade dilithium must be actively defended...