You are correct..the freewheel only isolates the rotor drive system from the engine. Depends on the design of the freewheel how much of the main transmission will be isolated from the problem.
Some helicopters, like the Robinson, have the freewheel on the input to the main transmission...Other designs have the freewheel inside the main transmission, allowing some gearbox failures to be isolated by the freewheel unit.
If the main gearbox fails above the freewheel, everything stops...as for the intermediate and tail rotor gear boxes, if they fail, the main rotor usually has enough energy to continue rotation after the little gearboxes fail...