Can you make it so that giving them a redstone signal will stop the damage to the rotor and stop it generating power by stopping it from turning?
Right now, the best way I can see right now is getting a sticky piston to push a block in the way of the blades. It works, but it's not a very IC2y way of doing it. It also turns out that that lets you generate free EU, as the Kinetic Generator doesn't update that the windmill has stopped 
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