Looking at the sentence structure I'm afraid it's obvioua toe he was still talking about the comparison of the two, he mentions both in the post, and the context of talking about the comparison is there.
Regardless, his/her interlocutor has hopefully had their eyes opened by the conversation, in which they said that even making the comparison was offensive.
According to the author of the comment your interpretation is correct, but it's far from obvious.
"Alcohol is unquestionably the more destructive of substances, LSD ranks far lower in this scale."
- The sentence comes right after he points to the chart of 20 drugs ordered by "harm score", where alcohol is #1 and LSD is #18.
- He says "of substances" without any qualification like "of those substances" or "of both substances".
- He mentions that LSD ranks much lower. However, both interpretations 1) "alcohol is unquestionably the more destructive of alcohol and LSD, because LSD ranks much lower than alcohol in the scale of harm" and 2) "alcohol is unquestionably the more destructive of all substances because it's #1, and LSD ranks much lower in the scale" are possible.
It's true - I was originally referring to Alcohol versus LSD (as that was what the parent was trying to compare, and couldn't believe that LSD wasn't terribly dangerous). But, I was prepared to also discuss the relevant merits of Alcoholic abusers and Heroin Abusers (and users) as well.
I think, much like people get used to the death rate from Car Accidents, and don't think of Cars as dangerous, people have gotten used to Alcohol issues in society, and don't think of it as dangerous, when it very much is. (Front page of New York Times is discussing an Alcohol related sexual also case in Palo Alto that almost certainly wouldn't have happened if the two parties had been sober).
Regardless, his/her interlocutor has hopefully had their eyes opened by the conversation, in which they said that even making the comparison was offensive.