I would imagine a skeptic would make the roll an opposed one, although true indoctrination would be in a place where the church can "make the most" of the situation (i.e. behind closed doors).
Atonement would definitely be possible, and may require the reverse process to be accomplished. The difficulty may be based on the length of time since conversion and how well they were "brain-washed" (DC may be the Priest's Bluff/Diplomacy/Intimidation roll as a base).
I would imagine though that from a Role Play perspective, the healing process would take day/weeks/months. Obviously Atonement as a spell may also have an affect.