The passengers could, by their closer proximity to the drives, sabotage the drives, or initiate the security system by remote control and infiltrate the ventilation system with gas to incapacitate the crew or something.
Putting the drives in the axial centre line would, however, allow the ship to ride on its drives: vertical, in this case, would equate with the direction of thrust, meaning that crew and passengers could easily walk about without need for grav plates, unless the ship had to evade or something - in which case everyone would have to strap themselves into crash webs or something.