This book makes an argument that the CIA developed the term "conspiracy theory" with the expressed intention of poisoning the well - that they introduced the term in the common parlance in order to brand those who might have more reasonable questions about important events with those who deny those events happened, or concoct preposterous explanations as to their occurrence.
This of course is a conspiracy theory in itself, and I wouldn't vouch for all the material in that book, but it makes an interesting point. I think it is common for people to express the argument that Mr. A made, and I do think it is an example of poisoning the well. However, there are certain cases (Flat Eartherism, Moon Landing Hoax, whatever convoluted Judeo-Masonic conspiracy is curently popular) where dismissal of Mr. B on their acceptance of such a conspiracy may not be valid logically, but I think it's more than understandable for you to want to call their judgment into question.
Remember though, there have been real conspiracies, and Mr. A's argument could in fact help to derail investigation into genuine wrongdoing (which was the CIA's plan all along!).
I would say you would have to take it on a case by case basis - it's a cliche, but "extraordinary claims require extraordinary evidence". Maybe hold off on branding Mr. B a "kook" until the conspiracy theory he's proposing has been shown definitively to be "kooky".