Just on the threshold of 2007 I found Droomkerk (Dutch for “Dream Church”) in Barsingerhorn, a little village just east of Schagen which is located approximately 40 km north of Amsterdam.
In a recently renovated church there are two luxury suites with capacity for 4 persons to stay (with a minimum of two nights stay). It looks promising, although their site is as yet only in Dutch. It is also fit for a small wedding ceremony and as a honeymoon suite.
Update December 2007:
I have deleted the link as it doesn’t work anymore. It is even obscure whether the project is still alive!