score:7
It is likely you are thinking of El club La Terrrazza (note the 3 'r's). You go up a hill through a quaint village with twisty sort of small streets to get there.
It's a converted villa rather than a cathedral, and the 'roof' you wrote about is most likely their balcony. The club opened in 1995 so meets your dating criteria of October 2000. Also, it has added new 'wings' and dance floors since your last visit.