Really? Yes. The Spanish Inquisition wasn't judged harshly for how many it prosecuted or killed. It was judged harshly (and sometimes unfairly as the article specifies) because of how it prosecuted people (by inquisition and with poor due process rights) and tortured people.
A defendant facing drug charges isn't going to be subject to an inquisition. Instead, he's going to have Fifth Amendment protection from testifying against himself (the complete opposite of an inquisition). He's going to be represented by counsel (even if he can't afford it) with ethical duties to him rather than to the tribunal. He's going to have a right to a trial by jury. He's going to have the right to appeal. Those make a big difference. And of course, if convicted, he's going to the slammer, but he's not going to get tortured.
Don't get the wrong idea. I'm not a fan of the drug war, but to suggest that it puts the Spanish Inquisition to shame is absurd - like Leftists who compare short-term family separation at the border with Auschwitz.