I feel like if Kilik had cured Amy's malfestation that he could do the same for Raphael, really. Kind of curious why that was even a thing, having that power to just cure malfestation is kind of ridiculous. And I would say Raphael's plot became about Amy after the events of SoulCalibur II, because it was Amy who nursed Raphael back to health, and they formed a bond over that, or at the very least, Raphael developed an unhealthy attachment to her and sought to repay his debt by devoting his life to her. It is true that Amy helped Raphael escape from the soldiers in the SoulCalibur II opening, for inadequately explained reasons, but Raphael didn't even so much as mention Amy in all of SoulCalibur II. Soul Edge really screwed him over. But yes, taking Amy out of the story affects Raphael's outcome pretty strongly. If she doesn't help him get better, it's possible that Raphael just breaks down and goes full evil malfested at the end of SoulCalibur II and perhaps becomes the next Nightmare, albeit as a beacon of madness instead of the cool and collected tactician that he is in SoulCalibur V.