Feel free to shoot this down, but what if William thought he was an orphan taken in by the Church, but the Old Wizard was William's long lost father? This would be something we don't find out until near the end of the game:
On the night of William's birth, screams echoed throughout the halls of the building. William's mother died during childbirth. His father, in a fit of rage, storms out of the building because he can't handle the pain. He ends up setting off on his own adventure in search of ancient magic described in the texts he had been reading, convinced that magic would have been able to save her. The church ends up raising William, and he turns into a bright student. Meanwhile, his father has traveled the world in search of magic. He seems to have figured out all of Magic except one missing piece - a piece that William provides when they meet again. His father does not recognize him, but when he hears his name, he begins to suspect who he is. Nevertheless, he keeps this a secret until some dramatic climax (possibly involving Will's dead mother) where the whole relationship gets revealed.