A dummy spell you replace the main one with, replaced again on a timer.
Ex:
Hide spell A on yourUnit.
Give yourUnit spell B.
Order yourUnit to cast spell B.
Reorder yourUnit's last order.
Run a timer to readd spell A and remove spell B when spell B finishes cooling down.
Well that's not neccessarily using cooldowns and wont show the timer, exactly... but I guess it would serve the correct purpose. Thanks for the input, PurplePoot.