It is well known that the ostensive purpose of prohibition -- the reduction of harm from drug addiction -- is not served by going after kingpins and cartels. There are always candidates to replace kingpins waiting in the wings and catching them only promotes violence as the candidates vie for status.
The effective policing tactic is to arrest middle class casual users and subject them to the shame of felony records and probation. You hunt down the soft targets at their homes and parties in vast numbers and hit them where they care -- in their job prospects, reputation, and freedom -- by briefly imprisoning them long enough to disrupt their jobs or school. Then you require them to report for weekly drug tests for years with a guarantee of longer imprisonment if they use unauthorized drugs again.
But the middle class voters won't support the drug war if you do that and there's no cash reward for cops in it or big media display either. So we're stuck with the wasted effort and public violence of going after kingpins.
And the credulous public always goes for the lie that the really important work is going after kingpins. Somehow it sounds meaningful to people who haven't thought about the subject. It's the opposite of effective policing, though.
I'm not in any way justifying his actions or anything like that. But I too was surprised that they just shut it down instead of just assuming control and going after what could have turned out to be cartels (assuming it wasn't just small time growers, etc.).
In case people have forgotten, SR itself was a target. There was pressure from Congress to shut it down, and it was probably the only goal of this operation:
Tor hides the source IP of people connecting to the server and tracking bitcoin transactions is pretty difficult as well.