@trollman, they did say that Otis was the one that would fish the walkers out of that mud and place them in the barn. Maybe Otis didn't tell Hershel about everyone of them since it probably happen shortly before the incident with Carl which took everyone's attention away from any recent additions to the collection in the barn. Plus the girl wasn't mention while Otis was still with us.











As far as Sophia goes I actually suspected something more sinister like maybe they used her to feed the walkers in the barn. But at the very end you just knew that she was the one coming out next
I don't think Shane froze at the prospect of shooting the girl, she wasn't a danger to anyone quite yet til Rick stepped right in front of her. If anything I'd go the opposite way and say Rick was trying to establish that he can do the hard things too so he decided to do it.
Also I don't think they needed this situation to play out to understand Hershel's dilemma. Andrea already had to shoot her own sister and they had to put down Carol's husband too even if they wanted to do that before he turned.