So, I've been rewatching the show, and something dawned on me. I've always felt that it was entirely possible that mother was the monster. It all makes sense now.

Mother was both the protector and the monster, therefore she was protecting the source from herself. She was doomed to live forever.

It was only when The Man In Black was born that she decided to kill Claudia. She then took the form of Claudia later, so that the Man In Black would join the other people's camp. She knew Jacob would stay. That is why she said that it was always supposed to be Jacob, and why she thanked The Man In Black for killing her. She effectivly split up her powers, the protecter side to Jacob, and the monster side to The Man In Black.