Yes, the digital download costs more than it should.
No, stores should not suffer if the digital copy is cheaper. It is NOT the same product. If you buy it online and download the game, you get the game. If you buy the box, you SHOULD get more than just the game. Different products, it is not the same. I do not see how they would even compete against each other. It makes no sense at all.
I think the game itself is a little bit expensive if we consider the amount of players getting it, that it requires a monthly subscription, and how much the game costs if you are buying your keys or boxes or whatever for the first time. If you buy the Battlechest (Vanilla + TBC) you pay 40$. If you buy WotLK you pay another 40$. Then you can get Cataclysm. It is expensive, honestly.