The partnership to be supported by Google Wallet and Apple Pay has nothing to do with payments at the store. Stores sign contracts with processing companies; the store seldom owns the payment terminal. The store is free to negotiate or decide what type of machine they will use, which types of cards to accept, and if they will accept conveniences like MC Paypass, Interac Flash, or NFC methods. The retailer is well within their rights to say they won't accept NFC.
The only thing they are not allowed to do is to decline to accept legal tender. I.e. they legally aren't allowed to reject a $100 if it is a genuine bill, regardless of what store policy is.