Their observation was that reputation mattered on SR a lot and a well-kept reputation was valuable at scale in a way that it isn't for being a street-corner pusher looking to stretch your buck by cutting your supply with adulterants. The smart play was to provide a high-quality product at a reasonable price (the latter being the easiest part since they were bypassing the obscene markup of official channels).
Yeah, I'm not saying they're less safe. In fact, on average, I'm willing to bet that the drugs sold on Silk Road were much safer than their street equivalents.
My point was about large sales: Silk Road moved not just personal drug sales, but also industrial quantities of drugs that were almost certainly re-sold. Those latter sales are impossible to track and (by volume) almost certainly represent the majority of "doses" sold through SR. Given that, I doubt the OP's assertion that SR itself represents a particularly effective form of harm reduction.
Or as another framing: SR gave tech dorks a way to buy cheap, clean drugs. But those aren't the people who really need harm reduction techniques; the ones who do are still buying adulterated drugs, which are derived from the cheap, clean drugs on SR.
What you say is also true. So there is a trade here. I'm not claiming it's "worth it," but the alternative without SR at all does seem to be more negative.