Ok, so here's how I know that Hershel had to know Sophia was in the barn in the midseason conclusion of the Walking Dead.

Season 2, Day 0: Herd event, Sophia is lost in the woods. During the search, Otis shoots Carl.

This is important.

Rick takes Carl to Hershel, who then begins the process of saving Carl. Otis and Shane go for the supplies at the high school. 

Back at the road, Daryl and Andrea go out looking for Sophia.

This timeline is crucial, because it's in this span where Sophia is bitten, escapes and dies, and then makes her way to the farm to be captured. This means Herschel and Otis or Jimmy, possibly someone else must have helped put her in the barn-- as that's a two, probably three person operation. One person on the leash, one person on the entry door to the barn, and one person on the far side of the barn, drawing the attention of the walkers.

She can't have arrived later, because the Atlanta survivors had set a watch, and would have seen Sophia being put in the barn. It can't have happened while Carl was being tended but before Daryl, Andrea, and Dale arrived, because Otis was with Shane, Hershel and Patricia were with Carl, Maggie was going to get Lori, which only leaves Beth and Jimmy to put Sophia in the barn-- which could have happened, but then Jimmy would have to be either the most mentally challenged 17 year old male left alive or the most psychopathically capable liar, because he then later joins the search for Sophia, working hand in hand with Rick to find her.

Which means Hershel and likely one other surviving member of the Greene family not only knew Sophia was in the barn, but allowed the Atlanta survivors to continue searching for her-- after Daryl's injuries and the loss of the horse, after seeing them deal with the possibility she was alive when finding her doll.

The only way they might not have known she was in there was if Sophia got bit fairly shortly after Rick left her, stumbled towards the farm before dying and reanimating and Otis put her in the barn, by himself, before going hunting. This seems impractical for the simple fact that putting a walker into the barn required more than one person to do properly, and the Greene farm survivors, whatever their faults, at least seem to have figured out how to safely put a zombie in the barn without having the whole farm get overwhelmed.

Soooo.

The most likely conclusion leads us to the fact that Hershel knew Sophia was in the barn, and purposefully kept that information from the Atlanta survivors-- possibly to keep them preoccupied while Carl recovered well enough for them to depart to Fort Benning, at which time he might have (presumably?) told them the truth and offered to keep her there in the barn until a "cure" was found. Given his view on the walkers, I don't think he would have staged a "discovery" of the girl, knowing the Atlanta survivors (tearfully) just kill her. Which, overall, makes him just about the biggest monster we've seen so far; a deranged, manipulating, lying old man who can't accept the truth of the walkers, doesn't have the charity to recognize a good survival situation when it pulls up on his front lawn, and is too cowardly to come clean once the ruse is up.

If the Atlanta survivors had known Sophia was dead right away, they could have focused efforts on cleaning out the surrounding area of supplies-- using the horses with Maggie and Jimmy, and then splitting the take with the Greene survivors while not placing as much of a burden on the existing goods. Daryl wouldn't have suffered his injury, and they wouldn't be "going through the antibiotics so quickly." The scrambled poop sandwich of Season 2.5 is going to fall squarely on Hershel's plate. His choices were reprehensible, and the consequences could be pretty bad, too, depending on how things continue.