Other than completely ignore (no newspaper or magazine subscriptions and no web site visits) the story, the only thing I can think of is to take a casual "yep, we did it, sorry, yep, you're right" attitude. Part of the reason this story has such legs is because it has created debate. When Pats fans go on the offensive (others do it, Bronco and 49er salary cap, little or no advantage, etc.) all that is doing is inciting a fan of any other team to prove you are wrong. Guess what, 31-1 are not good odds!
I remember a manger of mine many years ago telling me that it is impossible to win an argument with a customer. The rationale was that regardless if you win or lose the argument, you have upset the customer, which means they are no longer going to be your customer. By not arguing and simply agreeing with them they are unable to get mad at you. Same philosophy, as difficult as it is to employ, makes sense with writers and other fans. Yep your right, Patriots were wrong, they got punished. Rather than disagreeing that the team should be disbanded or whatever the person is trying to say, just agree. "Well, that's an interesting idea, I'll have to think about that, maybe you're right."
Look at it this way. Your customer places an order with you. Needs to be there overnight. Didn't happen. Are you better off talking about all the other orders that did get delivered, that your competitors also sometimes miss shipments, that they should have placed the order earlier in the day, that it was UPS's fault for not picking up the package? No, best thing you can do is own up to it, apologize, promise to do a better job, thank them for their business and change the subject.
Same line of reasoning goes with this debate. It's very obvious that rationalizing and defending the actions of BB are not going to sway other fans. The mediots are hoping we will do just that because that entices fans elsewhere to respond, which increases ratings and profits. If those fans of the 31 other teams have nobody to argue with then at some point the debate becomes boring - and the topic changes.