David Edding's Elenium series (the first one) is all about church intrigue. I'm sure it's not historically accurate, but it's a very easy read.
Fun series. Though I must say, Pagan gods granting spells to the church knights because their god (who's clergy is intolerant of both magic and other religions) refusses to do so - and pretty much everyone has a wink-wink nudge-nudge attitude about it? The author ran by that concept rather fast, and it's pretty tough to swallow.