There's definitely no stopping Silk Road nor similar websites. It's like Hydra, if you cut off 1 head 2 will grow back. Whoever runs these websites definitely needs to focus to enhancing their security to stay alive a little longer each time. The only problem here is that the media tends to abuse news like this, and the average Joe ain't really smart.
I'm hoping that this hydra effect keeps on multiplying. Maybe then the govs will just admit defeat and start to legalize and regulate their use. Just think of the good that can be done with the tax money. Everyone wins then. Ps. I also agree with you about Joe Public not being very smart but hopefully they'll get clued up and warm to bitcoin over time.