I'm not sure that CMU needs a warrant to collect the data passing over TOR. It certainly violates my ethical principles but perhaps the threshold is lower for others?
Intent will matter very much in this instance: If the FBI paid someone to do something for them that the FBI would need a warrant to do, then there's a problem. The same would be true if a warrant-less sheriff paid a private investigator to eavesdrop on a suspect.
Otherwise, if, in the course of their research, no matter who funded them, CMU researchers found someone doing something illegal and reported it to the Man, that's generally regarded as good citizenship. If, in the course of my research, I happen to unmask a bike-theft ring, you can be rather certain that I'll call the cops.
Tor is a good invention that needs our support, but it isn't a license to do illegal things.
Tor is, in many ways, an encrypted Twitter. You know that everyone can read what you send and some people will actively attempt to crack it. You bet everything on the encryption and network structure to avoid interception and localization. I don't think there ought to be any inherent presumption of privacy attached to the protocol; to assume that there is one is to be exposed to any breach in the protocol's design.
If you wiretap your entire neighborhood, find a bike-theft ring, and call the cops, you'll also get in trouble.
Hold on, what about wiretap laws?