What concerns me the most in this story was how the feds managed to bust into a highly anonymized encrypted network
You should remember that the TOR is not anonymous anymore. It has been cracked by the FBI. Out of the 4,000 or so TOR relays, around 10% are controlled by the FBI and the CIA. When you log-in to Silk Road, if your entry node happens to be any of these fed-controlled relays, then the feds will be able to track your real IP address.
Do you have sources for this? Though people shouldn't be using tor bareback either. Use a proxy or public wifi before you connect to tor and then you should be safe.