I just had one of mine (from Vienna) taken down on Alamy. The thing to remember is that any private place - a church, a palace, a castle, that you might tour, especially if you buy a ticket, can have its own rules about photography. Some ban photography altogether and have signs to that effect, others might have a sign somewhere that says no commercial photography. Their place, their rules! There is no "free speech" right to take a photo there and sell it, even under an editorial license. So they are well within their rights to request that it is taken down.
The question on whether you take the image down from other agencies is a matter of risk - you probably should, but you could balance that against the chance of discovery. The legal answer is - take the images down.
Steve