Yes, and while we are at it, let's compare the effects of pharmaceutical methamphetamine and pharmaceutical opiates. The unregulated production process surrounding black market drugs causes quite a lot of damage, and that damage could be eliminated by legalization and regulation.
There are some drugs that practically can't be used recreationally without major damage to the user. Mostly these are highly addictive and lead to self-neglect and self-destructive behavior, very unlike nicotine and even alcohol.
Legalization can't change this. What it might change is a shift towards less dangerous drugs to mob up the recreational drug market. SR however is not even slightly going in this direction, so the whole objection to the criminal nature of silk road is baseless.