It seems the real question is why CVS/RiteAid is not accepting CC via Apple Pay but does allow a magnetic swipe?
The MCX members are in a pretty tough pickle right now.
They hate credit card fees, but absolutely depend on credit cards as they make up the vast majority of payments in their stores (and obviously online). They don't want to pay the fees, but want the customers and the sales revenue, and that means taking credit cards.
Customers, meanwhile, overwhelmingly prefer to pay with credit or debit cards, since they have consumer protections, physical theft protections (a card can be deactivated, cash cannot!), and you don't have to worry about not carrying enough cash (or too much cash) when you shop.
So what's a retailer to do? There's only one way to give consumers the cashless aspects of payment they demand while not paying fees, and that's with bank account debits (ACH). Of course, there is no consumer-friendly mechanism to do that at point-of-sale... So they had to create one. Hence CurrentC.
However, CurrentC really only has a chance to work if people are not using something based on credit cards.. Hence the exclusivity clause that prevents CVS, Rite-Aid, et al from accepting other mobile payment systems. Presumably Google Wallet adoption was so low that its use fell under the radar - since they looked like normal credit card transactions.
However, Apple Pay arrived with such media hype and buzz that they had to pay attention to it, and when they saw reports that it was working in MCX member stores, well, they pushed the big red panic button. They know that with Apple and the big three card processors behind it that it has a very substantial probability of success, and that would kill CurrentC dead.
They also have to contend with two big possible ramifications, however unlikely they may or may not be:
1. Apple and/or Google remove the CurrentC app. CurrentC is then quickly dead.
2. MC/Visa/Amex decide to either not renew their credit card acceptance agreements with those merchants, in which case they have a serious, major, and immediate problem - or they simply twist the knife in a bit and hike their transaction fees as punishment.
I almost feel sorry for CVS and Rite Aid, since they are taking the bullet for the rest of the MCX team and really appear to have no recourse. However, since Meijer is both an Apple Pay partner AND an MCX member, maybe there is a way out for these retailers after all...