You make some good points, so I hope this doesn't seem dismissive-- my claim is not that the study is right. My claim is simply that the editors of the NEJM decided to publish the study having read it in greater depth than any of us here would care to, so if I read the CNN article and think there's an obvious reason it's not true, I can be pretty sure I'm wrong.

Now that being said, I think we're talking at cross purposes. The study found a link between coffee drinknig and mortality; I misread the GGP as being critical of that link, where it's actually just a hypothesis which would explain it. So none of this is really relevant :P