If feed is in the coop, moving it out to the run may help. I'd just catch them and eat 'em. 

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I found it very easy to trap squirrels and usually caught 2 or 3 a day. I used a med sized hav-a-hart and adjusted it a bit so it had more of a hair trigger. Smeared peanut butter on the trip plate for "glue" and sprinkled that with sunflower seeds. He could tie the door up for a few days until they get more accustomed to the trap. Squirrels can really do a lot of damage your house.My grandfather has the hardest time with squirrels. They get into his attic. He said they're too smart for traps, but that could just be the squirrel he has.
It's expensive, but you could switch to metal roofing.