Locks could be such that if used, the ship key itself is locked onto it, or retained within it (providing the door key is different), and can only be retrieved by removing the control lock.
If the control lock has a barrel and key system, then security for the ship is through taking this control lock key away after flying (plus the lock itself to a point). In fact, looking at the photos posted there, it could be done this way as the brackets already are, with a long-loop padlock... just remove the stupid weak-link pin.
Another way would be a cable looped from the lock round the upper of the cyclic via a sheath (for visibility, not necessarily the primary locking action) that can't be removed 'til unlocked, a la push bike lock.
The whole concept of building in a weak link is assuming the whole design itself is flawed I think, which it is from SilsoeSid's findings. An abortion. Personally, I wouldn't feel comfortable about attaching that thing if I was going to leave the machine for someone else to fly after me, checklists and procedures or not.