It was very poetic the way they all blasted the walkuhs away, after arguing they were no longer human, yet once they realised Sophia was now one of them nobody wanted to shoot her. It was clear Rick would be the only one who could shoot her, no matter how much Shane may try and undermine him, or shake his confidence, Rick is the true leader. The fact he still has humanity and cares for others isn't a weakness, but something to be valued in a world where the remaining survivors are becoming increasingly ruthless in their belief it's the only way to truly survive. But without humanity, what's the point in living? Shane is losing the plot, big time, that man is going to become a danger to them all!
I'm unsure whether Herschel knew Sophia was in the barn, since he wasn't the only one capturing the walkuhs and placing them there. I don't believe he would have allowed the group to stay on his land for so long if this was the case, he was slightly deluded but he isn't a bad man. He just wanted to keep those he loved safe in case a cure could be found one day. Ooh, and Sophia made such a beautiful zombie...I wouldn't have wanted to shoot her either!
One question, though, was Merle an hallucination, or real?? I think he was real, and yup I know he had both hands, but I never thought he chopped his hand off anyway.