Out of respect for Japanese "omotenashi", I won't call it greed... I do think most Japanese people would want to maintain a fair and equal pricing structure for all customers. In a better world, if the economy was booming and people were prospering, there might still be some establishments looking to earn more by fleecing and overcharging tourists. It's fine to call that greed, or taking advantage of demand inelasticity, or whatever.
But... here we are. Times are hard, I get it. Even with overcharging under a dual-pricing structure, tourists will probably continue to visit Japan if they can afford it. It's just a shame that the Japanese will probably have to compromise on some aspects of their omotenashi because of greater factors beyond their control.
Maybe by having a dual pricing structure, they'd be able to realize maximum profits. But not everything is calculable in dollars and cents... all you'd need are a few establishments to start vastly overcharging tourists for whatever cooked up reason and the reputation of Japan for tourists might soon become "nice scenery, nice culture, but the people there will overcharge you because they think they can exploit your ignorance, or just because they can..." - neither of which paints the Japanese in the best light, or the way they'd want to be seen, probably.
Source: Japan Today article
There are many places on earth that exist largely because of tourism. And encouraging people to go experience cultures outside their own is a good thing.
Places that only exist because of tourism shouldn't exist in the first place.