Since there were no handcuffs to restrain their actions, a member of the Guard Squad who was proficient in joint techniques simply dislocated the limbs of those individuals.
It might seem extreme, but it was just a matter of dislocating their limbs. Under normal circumstances, as long as the joints were not left dislocated for too long, any orthopedic doctor could easily put them back into place without leaving any after-effects.
Of course, the longer the delay, the longer it would take to recover after being reset. The time taken for restoration was directly proportional to the time spent dislocated—the longer the wait, the longer the recovery period.
If these individuals had been original members of the fleet, and something like this had happened, the Guard Squad members would probably just discipline them. Someone nearby could offer a way out, and they would then readily reset the dislocated joints.