Dumb question, but the author kept running a TOR node at a site he knew was under NSA surveillance? That doesn't strike me as very responsible...
And, hypothetically, the FISA authorized box was only getting traffic from the one site, and not the entirety of network traffic. The room 641A attack is far more problematic.
So, if I encrypt something to, say, three layers and sent it to some TOR nodes:
1-2-3
1 knows it came from me and knows to send it to 2
2 knows it came from 1 and to send it to 3
3 knows it came from 2 and to send it to wherever
No one point on the system, IIRC, is meant to have the information necessary to compromise the entire chain. Though, if you could compromise a sizeable portion of the network, you'd be in with a significant chance of compromising any given message - which I find hard to believe that the government hasn't done.