This is seriously one of the first things anyone in security would have thought up
Ah, the /. 30-second expert. Indeed, the TOR guys did think of that too.
Malicious exit nodes do not per se compromise TOR, though they are in a position to take advantage of some potential exploits (also, exit nodes are irrelevant to .onion servers) It's been known since the start that if an attacker both controlled the exit node and could directly tap your line, there'd be and endless stream of exploits possible - and IIRC the NSA had just such attacks in its arsenal. But that doesn't scale - you have to be actively monitoring a specific target to de-anonimize them, you can't do it to everyone. If the NSA actually got warrants when they did that to Americans [pause for laughter] I think it's a fine system.
TFA seems to be about taking over more than half of all TOR nodes, which can hardly be done in secret, and really makes 0-days in the TOR bundle visible.
Far more worrying, especially for the conspiracy theorist, is the never-ending stream of vulnerabilities in .onion servers allowing the operators to be de-anonymized. It's hard to believe TOR wasn't designed that way. TOR seemed designed from the start as a system to let Chinese dissidents use American servers safely, but not allow Silk Road-style sites (servers illegal in the US) to stay up. That IMO would be pretty cool if the US itself weren't growing ever more repressive.