The USG is not a monolithic entity. The State Department loves TOR, for the reasons you list, while Justice hates it. The Justice Department does not need State approval to get warrants and take down servers, nor do they need State approval to work with their foreign partners to do the same.
The US/EU governments run their own nodes. Why WOULDN'T they take down third parties that aren't willing to give them the access they need to sniff traffic? Their support of dissidents in other countries doesn't require private nodes to exist.
Feel free to drop the 'even' in that sentence. Just say the magic words 'child pornography' and the judge will go and install that bug himself. Tor has a very bad reputation in The Netherlands, I think just saying it's a Tor node might be enough reason for a judge to sign off on an eaves-dropping warrant.
Even on a more practical level, aren't all major hosting providers ones that follow standards where getting a USB drive onto a server would be extremely easy to trace back? Where was this guy keeping his servers?
As an European I expected the US/EU governments would keep their hands of Tor because dissidents use it in countries where US/EU want regime change.