The website Silk Road could very well have laundered money for terrorist organizations needing money to attack interests in the United States. Using BitCoins, users bought and sold drugs, weapons, porn, and more. The FBI didn't beat Silk Road--it joined them. The agency was able to indict and arrest the website's owners because the FBI hacked into the website.
Yes, the FBI should have shut down the Silk Road, because it contains a great deal of illegal activity. The Silk Road allowed people a means to do a great deal of illegal things. The FBI's job is to enforce the law as well as to investigate threats. The FBI was proper in its efforts to shut it down.