He chooses to work for an agency that breaks the law. Do we just turn a blind eye?
If he was answering phones there, it'd be one thing, but he's a cryptography expert. I'd imagine he'd be only a degree or two removed from something nefarious.
Just following orders is not an excuse if you have a conscience.
e - grammar
At any rate, if the NSA wanted to continue to participate, they'd just hire people not officially associated with the NSA.