It took them a few days to decide how to respond. According to Bleeding Cool they first tried to talk to DC Comics about the issue and they were stonewalled. And that's when they retaliated. B&N corporate sent an email to all stores and ordered them to pull all 100 of the titles covered by the Kindle Fire exclusive, including Dark Knight Returns, Fables, Blackest Night, All Star Superman, and Y The Last Man.
Don't worry; you'll still be able to order the comics and graphic novels on the B&N website, but you won't be able to pick up the novels in store.
This reminds me of last year during the early weeks of the Agency pricing fight. Amazon were fighting directly with Macmillan over the pricing issue, and Amazon responded in a manner just like B&N. They delisted all Macmillan they wee carrying and turned off all the "Buy Now" buttons. naturally it did not go over well with Macmillan, authors, or the book-buying public.Amazon eventually had to back down and apologize, but I'm not sure they've ever been forgiven.
Barnes & Noble might not have taken on as powerful of an enemy as Amazon did, but B&N also picked one that can afford to hold a grudge. DC Comics didn't have a compelling reason to get their comics on the NookColor, and now they have an emotional incentive to refuse.
Let's hope B&N didn't piss off anyone other than DC Comics; they need all the goodwill they can get.