Even though they were a puppet state it didn't mean that they liked it. For the most part their was little alternative for them but passive resistance and sabatage considering the absolute defeat of the French. The order to scuttle the fleet was given when the German and Italian armies were already surrounding Toulon to seize the fleet. I don't imagine the those in the French navy had enough manpower in Toulon at the time to secure the fleet entire fleet and escape with it for De Gaulles' exiled governent or the Allies. I doubt many would have been keen on handing the fleet to the Allies anyway considering the British sinking of the French fleet in Algiers following the Fall of France.