I don't know about churches per se, but a few of my friends did stay in a convent for a few days last summer in Paris (the name escapes me right now). They said it was great - cleanest they have ever seen, awesome breakfast included, etc. Their only complaint was that they had to be back by 10pm of they would be locked out. Basically - not somewhere you'd want to stay if you wanted to party all night.
"Growing old is manditory, growing up is optional"