The shoot action Captain Blackheart provides is tied to a move action, it’s not a full shoot action on it’s own. Think of it as Captain Blackheart having the generic captain ability with the SAC ability.
Per your scenario, if you rolled successfully with Crimson Angel, you would not be able to use the SAC part of Blackheart’s ability, but you would still be able to use the captain part of his ability (move and shoot). There is nothing that would prevent you from putting those crew together on the Harbinger, just be aware that you would not be able to give the Harbinger 3 actions in a turn, only 2 at most.