Walgreens has supported Apple's Passbook on iPhone since it launched, allowing me to always have my Walgreens card ready. Heck, I don't even
have a physical card. Sure, I don't get coupons through Passbook, but if I cared about that, the Walgreens iOS app presumably has them. The same approach (Passbook for the card, and a separate app for added functionality like coupons) should work for any other retailer too. Heck, if the coupon thing really is an issue, they could join together to come up with a common app for retailer coupons without trying to muck with payments.
Which is to say, store discount cards and coupons is basically a solved problem already. Trying to tie that to a payment mechanism just seems futile.