They also know what specific pages on the offending websites they accessed.

I'm wondering if the classified document wasn't about tor, but about the 'implants' aka malware that were leaked in the same set of Snowden documents.

I think as much as tor being broken in some fixable way, they'd like it known even less that the FBI installs malware on the devices of persons of interest who haven't been convicted of anything.

If they truly can't break Tor and they deem the person of interest important enough for "national security" then I don't think anyone who has studied history, American or otherwise, believes that they are going to throw their hands up and say "welp, that's it."