This is network-wide. They did not and could not target just Silk Road 2 and its users, they sabotaged the anonymity of every user and service on Tor.
A title 3 wiretap requires trust in both the government and network operator, which users of Tor may be avoiding for entirely legitimate reasons.
I agree that there is no moral distinction between a title 3 wiretap and Tor infiltration, however a title 3 wiretap is a passive listener while this Tor infiltration is not. The nature of the Tor infiltration caused anonymity to be stripped and readable by anyone aware of the flaw. They used resources unavailable to others to expose that information not only for themselves but to everyone.
The equivalent would be streaming a title 3 wiretap sans filter to everyone on the internet.
I'm not sure I follow the point about how the FBI could have done grave damage to everyone's privacy. It's (hypothetically, assuming this is how the FBI did it) the relay-early traffic confirmation vulnerability that did that. The FBI didn't create that vulnerability.
In what I think you mean by a perturbation attack, the attacker would deanonymize traffic by influence timing of packets on one end and observing the other end. Only the attacker learns anything. But in this attack, the hidden service directories found a clever way of broadcasting the name of the requested service, in plaintext, to the rest of the circuit. The attackers could read the message, but so could anyone else running a Tor relay.
Given that the message could have been trivially encrypted, that does seem like pointless collateral damage.
If the collateral damage you're referring to is loss of trust in Tor, that's not damage: that's new information.