They are an organisation made up of priests who are very dedicated to what they do, serving the Light. Priests pray and dedicate their time to God. They are not enemies of spook's, and not allies, but merely dislike them. The priests from the Church don't agree with the business that the spook's undertake, but are not neccecerily hostile towards them.
They are hostile to the Quisitor, who hunts down witches as well as spooks. An exception is with Father Stocks, who is not hostile at all towards spooks, for he did an apprenticeship with John Gregory, completing his time as an apprentice spook. However, Stocks turned down the chance to become a fully-trained spook, and instead turned to the Church as his occupation.