The Church is a powerful but weakening organization in Spice and Wolf. They appear to be Christian in nature.
The church loathes pagan deities or magic, primarily for their own self image and greed. This comes back to bite them a lot due to their suspicions of good people, like Norah, just because someone is proficient in their job or very skilled.
On one occasion, they attempted to kill Holo, whom was classified as a pagan diety or a woman possessed by a demon; she scared them off by revealing her true giant wolf form.