> Criminals (and worse) use all sorts of things, including technology, that everyone else uses. By your logic, the FBI should execute seizure warnings against GMail, Yahoo mail and Facebook... every time they have "evidence that criminal emails passed through that server."
They do, actually, except most of the time they don't bother with the warrant, and it doesn't make the news because neither law enforcement nor the companies involved have any interest in disclosing it.
If secure anonymization technologies become a lot more common, law enforcement organizations will eventually learn not to bother. Until then, anyone running such a service (such as a Tor exit node) should expect to have this happen to them periodically.