There's also the small matter of whether they should be using tax payers dollars to fund the development of a proprietary product. I realise that most people use Windows but it still leaves a bad taste in my mouth. And I'm not even American!
Now for better or for worse, Microsoft Windows plays a major role in US business infrastructure. So isn't it a good thing for the NSA to use its position to strengthen the USA against new attacks that, perhaps, only this agency has the ability to see coming?
I know they don't pay state tax: http://crosscut.com/2008/02/02/microsoft/11167/