Spending the money on the Silk Road trial on ads talking about how addictive and dangerous stuff from the pharmacy can be -- even more so than stuff on the street -- and that you need to be careful experimenting with medicines would likely do more to keep people safe from opiates than shutting down Silk Road.
(There's a similar argument to be made about stimulants and ADD/ADHD meds.)
Really, the only things that people can find on Silk Road which doesn't have a ready medical analog that's abused by people all the time is marijuana and hallucinogens -- the drugs on the safest end of the spectrum.
If your conjecture is true, and Silk Road gets people out of their pill cabinet on to safer things to experiment with, then it's actually making people safer to let them explore like that.
The problem with these debates is that drug policy involves a complex network of different pieces that are interlinked, and what seems like a straight forward solution to one issue actually ends up backfiring when the effects move through the network.