The TOR Project identified the specific problem and suggested that people who desire privacy must get the patched version of the TOR Browser Bundle, stop using Windows, and disable Javascript. If your Windows OS is compromised, which it clearly is, it doesn't much matter how you sign in to the Internet. And, according to TOR, Javascript was used by the NSA to breach an older version of the TOR Browser Bundle.
Some feel this entire attack is more about scaring people away from using privacy tools such as TOR than it is about fighting child porn because no actual pornographers were caught. They remained anonymous. TOR is still considered secure if used properly.
http://www.activistpost.com/2013/08/nsas-cyber-army-attacks-navys-tor.html