I find it plausible that the NSA, DHS may have assisted. During the same time of the rise of Silkroad we have the NSA in full cowboy mode. A reading of the xkeyscorerules100.txt[1] leak shows this, among other things. Looking to Tor as a potential tool for terrorism, if not now than in the future, they would turn to Silkroad as the only interesting target for them to train their teeth on. I just know that if I were in the shoes of a NSA "hacker" dealing with Tor I wouldn't be satisfied with playing war games against internal teams. Hackers are addicts that get their kick best when its public. I would certainly have argued for "better cooperation" with the FBI and DHS for that reason alone.

Anything the NSA does is "secret" so the holes in the FBI arguments, in this scenario, would make sense. An interesting result in this case would be if at any point evidence is not permitted for publication. I wonder if the defence could construct a canary for this possible circumstance.

1: http://daserste.ndr.de/panorama/xkeyscorerules100.txt (note how certain civil liberties are dictated by Geo IP location alone -- that is what I mean by "cowboy mode")