I have  taken many photos in cemeteries & have never had anyone question it. But your experience made me curious & I found this interesting article that discusses the topic in detail:

http://www.legalgenealogist.com/blog/2012/10/22/cemetery-photos-permission-required/

It mostly discusses the U.S. & Canada, but there is also some mention of other countries. The gist of it is that cemeteries can legally make "reasonable" rules about what activities to allow on their property - even if the cemetery is a public one. So they can certainly require you to be respectful & non-obtrusive. Not allowing photos at all or requiring prior permission doesn't seem reasonable to me, but my totally unprofessional guess is that they have a right to do that if they choose to be rigid. But I certainly wouldn't let this one negative experience discourage you from taking photos in cemeteries.