So here's what I can grok from it:
* "Freedom Hosting" founder has been arrested; presumably, many people were using "Freedom Hosting" to host onion sites (is this where "half of all Tor sites compromised" comes from?). No charges listed, article slightly hints at child pornography charges.
* Someone, presumably the FBI, has set up an exploit to be distributed through Freedom Hosting sites that will phone home and reveal your non-Tor IP address (solution: seven proxies). "Freedom Hosting" founder was probably coerced into allowing distribution of this exploit.
* Author claims that said exploit only affects Firefox >= 17 on Windows.
* There's a link to a paper about possible problems with hidden services, which is apparently not relevant to any of this other than the fact that there was just a shakedown on a big onion site provider.
I'm flagging this article because it is utterly incoherent and the headline is sensationalist. There is no evidence of a fundamental flaw in Tor being related to any of the events mentioned. Hopefully someone will write a comprehensible piece soon and put it out there.