As I understand this, the CMU team allegedly deanonymized SR2 in the course of their research, and then shared the information with the FBI. Once they had done that, they were allegedly forced to withdraw their Black Hat presentation. There's also the issue that the CMU team had NSA funding. I haven't seen any claims that the CMU team was initially focusing on SR2 and other "illegal" sites. But I wouldn't be surprised by that.
If that's what happened, it wasn't a wiretap. It was a tip.
The association of SR2 deanonymization with CMU's withdrawn Black Hat presentation is indeed speculative. But there's arguably more to it than innuendo. Time will tell.
It's well known that the DoD has funded Tor from the start. But it's at least decent of them to independently fund CMU to compromise it ;)