It's not going to be a fight.

The only reason that Souichirou was able to kill Medusa in the Unlimited Blade Works route was because he attacked her by surprise when she was not aware of him.

In a one-on-one fight, she would be aware of him, so she could just use Cybele or even Bellerophon to win this.

Moreover, unlike Saber (Artoria), Medusa normally fights with ranged attacks, so it's going to be hard for Souichirou to even attack her.