His powers can in fact be explained logically since he can manipulate matter on a sub-atomic level thus giving him the capability to open black holes or ripple space time itself. Reality is the purpose of the debate. Your character cannot be and is not what you call her out to be. She cannot rid the consciousness of atoms without eliminating everything since he can recreate himself. You have also argued against her omniscience.

She would know of any threat: so there would be no threat. She has full control of her 'life',

Then you say

although she doesn't seem to know what she wants to do with it.

If she is truly omniscient she would know what she wants to do with her life. Unless she is not omniscient like I have pointed out. She is not all powerful either since she cannot do everything. She is a creation by humans. She is a virtual being. That is a created substance. Dr. Manhattan is a creation of humans. They both are, but you cannot destroy Dr. Manhattan. He can teleport you anywhere he wishes. He can control her sub-atomic structure. She cannot stop that regardless of what she tries to do. That is something that she cannot control. He is stronger than Lain.