If the church is aware of Daina's holy power during this time already, I expect them to try and lock her up to hide her from the duke once he mention his plan to adopt her.
Maybe as a safety measure they'd incite one of the bullying kids into doing it so when the duke find her they have someone to blame.
EDIT: The hints from the prologue are:
-He paid money and take her with him.
-The bigshot of the church come demand her back, so much like ch 1 suggest it seems only a few people at the top are aware of her true value.