Mary Lou Barebone doesn't just hate Credence for being a witch's son, she hates him for being a male omega on top of that. Alphas/omegas are already uncommon (and therefore "unnatural and sinful") and female alphas/male omegas are rarities among them, making them even more "unnatural and sinful" in Mary Lou's eyes. She hurts/punishes Credence for every little sign that shows he's an omega, none more so than when he goes into heat. Viewing his heat as the most sinful part of an omega, she locks him up in the most monstrous chastity device she can find every time he has a heat to keep him from doing anything sinful, which just results in Credence clawing his fingers bloody trying to get it off during the height of his heats.

Up to anon if someone discovers what Mary Lou does to her omega adopted son and rescues him, getting him somewhere safe and helping him through his heat instead of torturing him through it.