I think the problem here just comes from the fact that there was a rather abrupt shift in management.  I'm sure we can work something out.  As for Pepper, as a mercenary I simply assumed the Captain would have already hired her beforehand in order to ensure the new ship's safety.  Getting the "best of the best" to ensure a smooth maiden voyage, as it were.  For characters whose backgrounds depended on them already being a member of the ship, perhaps that could be reworked to state that they had already worked with the Captain previously?  That way they could be played as "established members of the crew" right from the get go, having a personal involvement at the start.