Samus would screw attack Kratos to death. He can never get near her thanks to the speed booster and shinespark anyway. Her range of fire is far is far greater as well.
And if he's up against phazon samus he's dead or corrupted after one shot. Plus she's litterally invincible in hyper mode. She can even drain his life energy. Or pump so much phazon into him that he explodes.