If you restrict the air that goes IN the supercharger, it makes less boost, less heat, and takes less HP to turn.
A waste gate will not work on a crank driven supercharger, the waste gate vents exhaust gas past the turbine of a turbocharger into the exhaust pipe, to keep the turbine from spinning the compressor faster so that it does not make as much boost. There is no exhaust side turbine on a crank driven supercharger.
As far as the original question, if you were to continue to over boost an engine, as you would if you left a two speed blower in high altitude gear at low altitude, you could easily destroy the engine. The excessive manifold pressure generated would make the engine detonate itself to pieces, probably knocking the rings off of the sides of the pistons, crushing the rod bearings, caving the pistons in, and seizing the pistons in the bores. Odds are, a Merlin rated at 80" of boost might make well over 100" of boost if the blower were left in high altitude gear. That kind of cylinder pressure could easily destroy the engine.
I thought I remembered reading that the two speed superchargers were commonly shifted by an aneroid bellows.