Your group is telling a fictional story set in a fictional space-fantasy setting, not writing a manual on proper starship maintenance and security procedures.
If I have a player who wants to stay behind to "guard" the ship, I'll ask him what he plans on doing while everyone else is out adventuring. If he can't come up with an answer other than "guarding" I'll remind him that we, as a group, decided to play this game with the reasonable expectation that every player is going to participate in the story. Metaphorically staying behind is that player abdicating his responsibility to participate with the other players.