Magneto said to Psycloke "But you WANT JUSTICE, you want to BE JUSTICE. The boy inside of me will always UNDERSTAND that"
I think it`s pretty clear he`s saying that Psycloke wants to bring justice for the world and he unsderstands that sentiment, so much that he told Psycloke she can get out of krakoa anytime she wants because he trusts her and her motives, that`s big coming from him, so no I don`t see it as him giving her permission to lord over the world as a "big brother" but him trusting her because she wants to do good for the world for her own conscience not because she was given a mission. This reason alone made this issue my favourite from this series