The lawyer quoted in the article appears to contradict this: “Collection under this program was a compulsory legal process, that any recipient company would receive.” That's not a black bag job.
Joe who used to work at Ft. Meade – totally stand-up patriot! – is a senior employee in the company's operations department. He is served the compulsory process, and it is implied that under the process, he should not tell anyone else at the company, including superiors and company counsel. In fact, the senior executives may have even tacitly employed Joe for this role for this very purpose: he's been pre-vetted by the security state.
That's not quite a 'black bag' job. Nor is it completely legitimate. It's something in-between, which most of the time lets everyone work under convenient fictions, getting on with the rest of their jobs.
The example is "senior employee in the operations department". Probably, the same person who'd be asked to implement the tap if it went through CEO-counsel-VP-etc. The NSA might just be doing everyone a favor by fast-forwarding past those steps, since they can't say no and only face more risk for knowing more anyway.
But to consider another variant, I could absolutely see a janitor becoming convinced by men with badges that he must cooperate with their investigation, perhaps by planting a bug or offering out-of-hours access. A janitor could also be convinced by official-looking (and perhaps even truly official!) judicial paperwork that says he's not allowed to tell others.
In the case of my hypothetical 'Joe with Ft. Meade experience', the cooperation is cheerful because he believes in the mission and legitimacy of the request. But under the strange logic of compelled secret compliance, lower-level employees might be coerced into cooperation. (That'd be more likely to be seen as a true corporate infosec failure, rather than a "wink, wink, 'failure'", from the perspective of top executives.)
