Ok, my theory is that Hershel didn't want them going anywhere near the barn because they have zombies in it. Given that he's a very religious man, I can see why he wouldn't shoot them but just lock them up in the hope of finding a cure.
My second thought is that they knew there was a zombie in that well. It looks like it was there for a rather long time and how could they not have seen or heard it before then? Makes me think that is why they sent the group over to that particular well to get water.
My 3rd thought is that the girl wanted to get with Glen to get pregnant.
My final thought is that Lori is pregnant with Shane's baby. Based on the timing of the whole thing, it seems more likely.