First, I'm quite happy that this activity does not appear to be the result of wide scale infrastructure sabotage.
And I am quite happy that the FBI is doing its job to combat crime that is facilitated using (abusing) the technologies that are bastions for free speech, privacy and whistleblowing.
Of course the flipside is that this means that there are capabilities in place to disrupt anonymizing technologies - the technologies make investigation more expensive but ultimately are merely an inconvenience to the powers that be. So when it comes down to it, anonymizing services and Tor can't be trusted to secure you if you have something to say where your life is in danger.
The FBI (/others) wants the court system to replace technology as the gatekeeper to investigation. The court system, however, is brittle. It takes time, it fails, and it responds to external pressure - there are repeated studies that show that the length of time persons in US court systems are convicted to serve is highly correlated with how long it has been since the precising judge has eaten his last meal. There are also extralegal rights that law enforcement are given by legislature and evolving interpretations of what both these legal and extralegal rights entail.
But law enforcement also is justified from their perspective. They don't want there to be criminals that get away with crimes simply because criminals load up some software that obfuscate their identities, locations and accounts. If you look at this published list there are criminal organizations that you and I as taxpayers do want taken down. (I recognize that the sale and consumption of drugs is a greyer area of morality as drug use is sometimes victimless).
I think that for the most part law enforcement is capable of taking down these services and organizations other ways - ordering assault rifles and monitoring the drops - and that this provides opportunities for the government to enforce the law without sabotaging communications infrastructure. Taking down some .onion addresses doesn't do too much besides annoy the services for a time anyway unless the services operationally are not capable of standing up a new address and communicating with customers anonymously.
All in all it's a blurry line but I feel safer with places that are anonymous and secure than I do by trusting a court system and legal process that can only see, process, and be accountable for so much.