Perhaps.  But conceptually it doesn't make sense, especially in a game like Sins.  Basic example: If your fleet commander gives you an order, that order stands even if your engines get cut by an Ion Bolt.  Though Ion Bolt is the least annoying of those abilities.  Instead the ship defaults to its basic auto behavior, which is usually to attack the overwhelming fleet about to tear it apart if it stays behind.  This is mitigated somewhat if the ship in question is part of a fleet, especially if the fleet flagship is already leaving(or has left) and fleet cohesion is set to tight.  But if the enemy happens to hit your flagship with said abilities...