There are many ways bitcoin could be used in physical stores.
Some guys here are planning on creating printed bitcoins, using QR code or stuffs like that.
An other possibility would be to do everything wia wifi, for instance using smartphones running a full bitcoin client, or using a web interface such as mybitcoin.com.
I personnaly think the best would be if each store could act as a bitcoin bank. Basically you would have a bitcoin account in the shop, and you'll use with conventionnal banking-like transaction for every day purchases. You would only transfer bitcoin something like say one in a month, just to fill up your account. Such accounts could also use David Chaum's digital cash, so that stores could act like private money issuers.
I don't think bitcoin will put a end to banking system. On the contrary, it will democratize it.
Yes, bitcoin will democratized things since it does played the real role of genuine democracy which the world need. Concerning the payment issue there are many new project which have different set of bitcoin payment protocol which will make bitcoin payment physically to be seamlessly. However, bitcoin will not totally end banking system but it break the use to bank into 5-15%.