The electric starter uses a sprag clutch on the crankshaft to crank the engine.
This is a one way clutch which allows the crankshaft to rotate freely in the normal direction.
The sprag clutch installed on pre 2009 RE's is notoriously weak and, although it works for a while it has self destructed on more than one bike.
One of the chief reasons for it to break is these big singles will often kick back during shut down as the piston tries to compress the last fuel/air charge while coming to a stop.
The backwards rotation this causes will lock up the sprags and direct the energy into them and the starter gear chain.
That often results in a overload of the sprags causing them to shatter.
This danger really has nothing to do with using the electric starter although if the clutch sprags have been slightly damaged, the impulse shock of the starter being activated could be enough to result in their breaking.
If they break, their bits of hardened steel will get into the moving parts of the engine causing no end of damage to the gears, roller and ball bearings, sliding piston rings and sleeve bearings etc.
One idea to help minimize the damage the crankshaft reversal during shut down is, when you want to turn the engine off, use the Decompression lever to kill the engine while it is at an idle. This will prevent the compression kick back and this same idea has been incorporated into the new fuel injected models (although with them it is done automatically by the new design).
Anyway, it is a good idea to use the kick starter to start the engine whenever it is practical to do it. Save the electric starter for those (embarrassing) times when the engine dies at a stop light.