Question: Was Will the one who murdered his wife, or was it Stewart in an attempt to get Will charged with murder, so he could get his job back and not have to deal with Will anymore?
When Charlotte met Will in the hotel lobby about her "mistake" with Stewart, she said that she would talk to him about it. Will refused to listen and told her to keep away from him. He didn't want to be anywhere near Charlotte, and after she left the hotel, she probably went to talk to Stewart anyway. Considering the kind of person he really is, he murdered her. It was even said that there were more deaths besides her, all done by Stewart.
I also think it was Will, out of anger because she cheated on him.
Answer: It was Stewart. The wolf, as Dr Alezais says, removes everything from a person except for the person's nature and heart. Stewart, when talking to Laura at the estate, states that she knows what happened to Charlotte, which was his subtle way of saying he had murdered her.