He mentioned in the first episode we meet him something about someone finding a cure. When Rick mentioned the visit to the CDC Hershel still seemed insistant that someone will find a cure.
I imagine the barn contains family and friends lost to the walkers who Hershel believes can be brought back once a cure is found. He probably doesn't believe they are dead, but more like victims from "28 Days Later."
I see. So Hersechel doesn't believe they are dead. That Herschel wants them to disarm on his property makes sense now to the storyline. And now why he wants them to leave.