Well, create a dummy spell based on thunderclap. If you want to add the cooldown to the passive just remove the passive and add the dummy spell. Order the unit to use the thunderclap (it won't stop the unit) and start a timer. When the cooldown runs down remove the dummy spell and give the passive back to the unit.
Ghan has said he has fixed this. Monovertex please confirm this fix. This was only a problem with people that had signatures in the upper levels like not the special members but the respected members.