Prime isn't beating Dark Phoenix. There's a big difference between soaking up sunlight for 800+ cenuries to charge a biomatrix and being an immortal damn near omipotent primal cosmic force of life and fire that snapped and went evil.
Phoenix took down D'Ken after he had merged with the M'Krann crystal and become one with the universe. I think she can take a sunbathing Superman. Dark Phoenix mindwipes are permanent.