This book does not concern a conflict of faith, so much as a conflict of how that faith is practised. Joe Kiem grows up in an old Amish order, with its arbitrary demands and rules. He loves his family and his community, but he comes to realize that a faith in God does not require man's rules and demands, especially when they actually cause him and his family to be punished for following a different path to their faith in God. His questions are considered to be against the rules and rather than cause his family any grief in the community, his family chooses to leave the Amish.
That is an awfully hard decision because it means he and his family will be shunned, until he apologizes and returns to the fold - which he can no longer do because it would be going back to what he was questioning. So his family is forced to start a new life. And Joe comes to realize that while his earthly family is out of touch, his spiritual family is alive and flourishing and he finds fulfilment outside the Amish, moving into a Christian ministry.
We honour all sorts of people for bravery. This kind of bravery is rarely acknowledged, yet it is not courage in an instant moment, but courage in a minute by minute by minute life. A good book to read.