They can adjust the radar for this just like any other hindrances. (like ground clutter, buildings, etc.)
Or they could also coat the windmill blades with the same stuff used on our Stealth Fighters.
Animal Rights activists won't like it because they'll chop up more bats that way.
But who cares? Those creepy little cave critters spread rabies anyway.
We would likely all be sick without those *critters*.
They are very necessary for the elimination of mosquitoes and other pests.