question your assumption that you need to respond in the first place. You have no obligation to spend your energy on the "troll or functionally illiterate person" coin flip. to put it another way...

What I want is to say something that quickly quarantines the misreading comment in people's minds so the misreading doesn't infect the entire thread.

if for the sake of example we ignore the possibility that your writing actually was unclear or ambiguous, then for the misreading to "infect the entire thread", the other readers would have to have similarly poor reading comprehension, right? that or they're putting little enough effort in not to catch the original response being way off base. if that's the case, is it really that important how you are perceived?