The mother of Leopold (and his brother) dies in childbirth (and the newborn, being mutated, is immediately suffocated--this is a setting where infanticide and intense ableism of congenital disability is a thing). After the big switch, Francis himself is held through a kangaroo court and burnt at the stake, and while his brother helps redeem him, that redemption is at the cost of Leopold/Francis being whitewashed and the brother being imprisoned for "heretical" statements about him.

This is a post-apocalyptic story about religion justifying war and atrocity when it suits them! I didn't consider it a hard read, despite this comment, but keep that in mind!