I’m the author of the article. Sorry not to have engaged sooner; unrelated events made it impossible.
My article is actually very cautious and conservative. I don’t say that mathematicians should refuse to work for the NSA, or that learned societies should expel members who work for them. I merely point out that they could.
Mathematicians who cooperate with the secret services (e.g. department chairs who give their staff leave to work for them) may not even realize that they’re making a choice, because a culture has grown up where it’s unexceptional. I wanted to point out that it is a choice, that we’re not obliged to cooperate with the NSA/GCHQ unquestioningly.