Journalists, as a rule, do not wish to compromise their sources. The reason being that if they do, and if the fact that they have done so gets out, it makes it much harder to acquire such information in the future (and such information is what journalists ultimately want - the scoop). This has been demonstrated several times recently as journalists have resisted revealing their sources until strongarmed by the law.
The NSA (or whatever) would have to be offering a HUGE incentive/threat to the New Yorker in order to convince them to offer a deliberately compromised service. Admittedly, this could have happened, but I don't think any government agencies would be willing or able to offer sufficient incentives for the New Yorker to do that, given that they probably wouldn't get that much out of it.
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