Short answer yes. But not because they have a backdoor into the blockchain.
Internet traffic monitoring and profile analysis. Its really basic: x goes to y and initiates port traffic from x. Y deals in bitcions, therefore this traffic pattern is coin. Profile updated.
The same thing keeps coming up with TOR over and over again as well. "Can you be followed?" Again, this depends on how you use and start TOR.
Personally, if they had a method to corrupt the chain they'd have done it already based on the tinfoil hat crowd. Since crypto currencies, esp btc at current, could destabilize the currency the NSA helps to protect. They've been pretty blunt about helping on banking issues in the past.
