It would be more honest if you had added that double payments were the fault of one credit card company (ApplePay told them to make a payment, but they paid twice), and that the two companies disabling Apple Pay did this because they joined a consortium that is developing its own ridiculously complicated payment system that gives the merchant direct access to the customer's bank account (which in my opinion is totally unacceptable), and allows them to gather and analyse all information about payments the customer makes using this system. So all in all a system that no customer would want. The exact opposite of what Apple is doing, where they have the major selling point that nobody knows what you are doing with your money.
Now if I had just bought an iPhone 6, had set up Apple Pay, and I found out that a company doesn't just not support Apple Pay, but deliberately made changes to their system to stop Apple Pay from working, I'd be annoyed in a major way. I don't think their decision is good for their sales. At the moment this is probably not a problem yet, but the percentage of customers owning an Apple Pay capable phone, and the percentage among those who use Apple Pay, will be growing and eventually it will hurt them. Give it a year or two, and their systems will be back working.