You note time when the heavy gets airborne. i.e 45:00
add two mins= 47:00
take 30 secs off that= 46:30...this is the time you clear the medium for take off knowing that by the time they rotate, the 2 mins will clearly have passed.
Your initial assessment is correct, to wait two mins THEN clear for take off would cut into an airports efficiency a hell of a lot, and i know nobody that does this.