Begin tracking and disrupting the node networks via which blocks are propagated. Run tainted nodes which track IPs submitting transactions or full-clients requesting blocks, use Tor traffic analysis to work back to any cloaked users. Disrupt the IRC channels that allow bootstrapping, poison P2P listings. ISP-level/backbone-level deep packet inspection to identify nodes (doesn't need to be unencrypted, you can fingerprint connections from deep-learned traffic analysis and connection characteristics, see: Great Firewall). Then traffic/network analysis working from known nodes to identify other likely nodes in the network. General attacks on any crypto services or infrastructure advertised in public fashion (eg light-client providers, exchanges, tumblers).
(the NSA has all these cool toys... it'd be a shame not to use them!)
You can also make it virtually impossible to interchange cryptos into real cash, which guts the utility of it for most users. Ban exchanges from operating or offering services to customers in first-world countries, extradite those who persist. Sting operations on local-btc transactions. Apply RICO/war-on-drugs style roll-em-up tactics on those who persist - you're going to jail for 20 years unless you give up someone worth knowing or help us break some network worth breaking. The achilles' heel of the crypto world is that it's anonymous until you try and do something in the real world, and the financial system is an obvious point to attack from.
If we can take down Silk Road, we can take down other things in the crypto-world as well. I'd much rather our law enforcement concentrate on fighting a War on Cryptocurrency than a War on Drugs. Would certainly take cooperation from most of the first world as well as China, but China already imposes some pretty draconian stuff on their internet users. They're not thrilled with people using it to move money offshore, they're not thrilled with all the crypto users stealing electricity, they'd probably be down for cracking down too.
Oh yeah, legalize a bunch of drugs and decriminalize everything else, and you pretty much gut the crypto-economy. A massive amount of the crypto-economy centers around Silk Road-style operations and you can easily gut those with the stroke of a pen. Most users stop caring and the crypto-economy then largely collapses. The number of people who actually want murder markets or kiddie porn and are willing to do shady cash-for-bitcoin deals in a van in a Wal-Mart parking lot is not enough to actually sustain the market on their own.
Crypto only works because there's a veneer of legality, drug markets that people want to access, and relatively easy interchange to and from FILTHY GOVERNMENT FIAT, and we can nuke all three of those. Then you just clean up anyone still stupid enough to participate.