I think we all need to look beyond this individual battle/issue and look at the much bigger fundamental war that's about to be waged.
This isn't about CVS not liking Apple Pay or iPhone 6 users. Frankly, it's not even really about Apple at all.
The whole Merchant Customer Exchange initiative is about trying to cut the credit card companies and the hundreds of billions spent on transaction fees out of equation.
The thinking is that if they move to an MCX barcode system (via the CurrentC app) that's linked to your ACH bank card or store card number they save money on every transaction.
The advantage to them, in addition to saving billions in transaction fees is they get to harvest customer data on every sale. Similar to the 'reward card at the grocery store', Target, Best Buy Walmart, CVS and other members would be able to gather (and potentially share) data on all of their customers.
They will likely link some sort of discount/rewards program to it. It may be individual item discounts like grocery stores. It could be a flat discount (3% of purchases) or even a cash back program. Remember, they are going to save potentially billions on transaction fees..so giving some of that money back is a smart investment to encourage use.
The big battle that's going to be waged will be on privacy/security. I expect Visa/MC/Discover/AMEX and now Apple to team up on the front of EMV and Apple Pay solutions allow for anonymous transactions and are more secure than CurrentC. They'll especially play up the idea that your personal buying habits are being stored, shared and shopped. They'll also push the risk of potential exposure of your personal bank account info and question what fraud liability is in place. When debit cards first hit the scene, people were very wary about it being directly tied to their checking account. Limiting fraud liability helped people get over that hurdle.
As a customer I have mixed feelings. We all pay a higher cost for goods/services to mushroomed use of cc/debit cards. But I question how much savings we'd really see under an alternate system and question the privacy/security protocols that would be put in place.