That didn't stop him from banging those chicks on the ship so hard that it shook the room. He's a former demi-god, current full fledged god, he doesn't have to be attractive.
Her best chance to win would be to not use one of her normal weave summons. The dragon one is basically another version of the Hydra, which Kratos could handle, and the bird's not much of a threat to him either. Her real heavy hitting summons would have to be the centipede and the tarantula. But, Kratos would go full god mode, so it isn't like they could just crush him.
I can't quite say she'd get the best (final, Pluto to Sun punching) summon off because it looked to me that she combined powers with Jeanne to summon it.
The main edge Bayonetta has is she's far, far quicker than him and uses guns, that alone don't do much damage(talking about in gameplay) but she can spam them throughout all her combos. So for that I'll give her the edge.
God Kratos is when he was a full God at the beginning of GOW 2, and Bay prob still wins as she is both fast, has an incredible reaction time and can slow time after a dodge anyway. She would prob best use her sword as it leeches the soul and have those firery/lightning claw things on her feet.
She would prob win through attrition, she can last far longer than he can.