While it's not technically a children's book, it was adapted into a cartoon series for Channel 4 in the UK in 1992.
Here's why your description fits:
* Unusual: The story is a blend of mystery, dark humor, and the supernatural. It's definitely not your typical children's tale.
* The Minor Canon: This refers to the protagonist, a clergyman who finds himself entangled in strange and dangerous occurrences.
* Odd mix of religion and magic: The book deals with the supernatural, but it does so within the context of a church and the life of a clergyman. This unique combination makes for a truly unusual story.
It's understandable that you'd remember it as a cartoon. The animation style was distinctive, and the show captured the quirky and slightly unsettling nature of the original book.