There is no doubt that the CP sites / silkroad exist(ed). But the way the government handled it went beyond what should have been done.
Let's take another hypothetical situation. Lets just say that instead of an internet site, the silkroad was actually just a building. The government knows that they have to shut down this building in order to stop illegal activity. Instead of simply shutting it down, they take it over and put a sign in front of it that says "Closed for maintenance! Come back later!", and then they attached a tracking device to anyone who approached the building during that time (without them knowing).
This is basically what has happened here, and it's not the first time it's happened either. While you may say "Yes well they were just trying to catch the people who were going there", you must realize that there is another underlying reason to them handling it in that way. This didn't just affect people who were going to the said illegal sites, it affected plenty of (innocent) people who simply use Tor as a political statement against online tracking.
I'm pretty sure the government frequently delays busts on actual buildings/places in order to catch more people by staking out the location. On the Internet it is just easier. In fact, the tracking cookie
helps innocent people. If there were a real building the feds might have to track down and interview every person who went there. That might be inconvenient or embarrassing for an innocent person. On the Internet they can simply give people a cookie and wait a few weeks or so. All of the innocent people will automatically be determined innocent and they won't even know it.
