Actually, I never noticed anything out of place with the temples and shrines in Japan. Houryuuji (with the oldest wooden structure in the world) prohibits anything inside its temple grounds; there was no vending machine inside Toudaiji; same with Touji, Byoudouin, Nanzenji, and so on. The worst I noticed is just the thousands of tourists coming through to visit all of those places, and to that end there were stores and vending machines
outside the temples. At Nanzenji (and other Zen temples) it's probably harder to tell because some may not be able to identify the "main gate". In many temples there aren't even bathrooms inside the temple grounds, and signs warn visitors to use the outside bathrooms in advance.
Overall Japan does a pretty damn good job of protecting its national and cultural treasures. The only real distraction are the hundreds of school girls that visit temples like Kinkakuji, taking pictures with their keitai
