The FBI isn't dumb. They know that 10 SilkRoads will popup in the vacuum they just created. And those new marketplaces won't make the same mistakes SilkRoad just made.
Once they found the server, they had an all-access pass to the most popular black market in modern history. They could just sit back and make bust after bust after bust...
But instead, they exchanged their Palantir for a single arrest of a 20 something San Francisco nerd.
It's the same reason why they offer plea bargains to low-level drug dealers if they'll give up the people above them in the supply chain: it does more damage to the overall network to take out the one person it all hinges on than to take out lots of people out at the fringes. The network has to reconstitute itself, which is slow and expensive.
You hit the nail on the head there. Nabbing the "Dread Pirate Roberts" is definitely a career making move for any moderately ambitious investigator or district attorney.
The FBI is just a collection of people. Some dumb, some smart and most fall somewhere in-between.
My guess is the person(s) responsible wanted this on their performance eval ASAP so they can try to make a promotion.
That's just a wild guess of course. Without knowing the team responsible for the bust it's hard to know what the long term goal was but my experience with government work is that most employees are more concerned with their career and paycheck than long term safety and security of the public.
Maybe a winning black market site skyrockets rapidly, or maybe this causes trepidation in users and vendors who try to approach things more carefully, test driving many sites instead of flocking en mass to one particular site.
I don't think it's a foregone conclusion that a Silk Road replacement in terms of size and volume will appear in the vacuum; eventually yes, but I'm sure it's probably bought them a few months or years of disruption.
If the FBI sits back, they become complicit in whatever illegal activities were happening. Then you can have situations like the ATF gunwalking scandal (http://en.wikipedia.org/wiki/ATF_gunwalking_scandal) in which the ATF was trying to track smuggled guns up to higher-level suppliers, and had one of those guns used in a murder.
This would presumably go so far as the FBI asking other agencies to cease investigations which might compromise their larger operation. At some point, they will have to act.