Did I mention that she can destroy a dimension? She could destroy which ever dimension that Hyrule exists in and obliterate it from all of existence. Everything would dissipate to dust and become nothingness.
Not even Din, Nayru, and Farore could do anything to stop this. They wold perish with the destruction of their plane of existence.
Quite effectively, Samus didn't just trash Link in the process. She brought the whole Legend to an end!