Wow. Just wow. So the judge, who admitted to being ignorant of the real methods used to gather the intelligence, just throws out the 4th amendment without ceremony.
The government literally designed and deployed malware. They're no better than a Russian hacker or some Chinese teenager scraping passwords from popular sites with brute force attacks.
This is heartening in one aspect: the government is outright proving their inability to get through security layers meant to obfuscate traffic. Now, if you're browsing child porn sites, you deserve to be thrown in jail, but the fact that they're netting innocent users of Tor is disgusting.
Your best bet is to use virtual machines to browse, apply MAC address spoofing and change your MAC pools on your virtual hardware as often as possible. Oh, and of course, keep your damn software up to date!
The defense should have responded with what I used to, which would inevitably get the judge too upset to speak for a short period of time:
"Objection, your 'honor'. Court may not insert personal opinion in lieu of the facts in this matter."
Be prepared to be threatened with "Contempt", however.