The idea that the CIA popularized the term "conspiracy theorist" to stop critical thinkers from asking questions is, in itself, a conspiracy theory.
There is no evidence that the CIA popularized or invented the term "conspiracy theorist" or "conspiracy theory." It is not very likely that a government organization could intentionally popularize a term or phrase. Furthermore, there is no evidence within "Countering Criticism of the Warren Report" that the CIA was planning to popularize the term "conspiracy theorist" or indeed that the organization invented it altogether.
The Warren Report (1964) investigated the assassination of President John F. Kennedy: the death of whom sparked innumerable conspiracy theories. The memo titled "Countering Criticism of the Warren Report" (1967) addressed the public suspicion about the investigation.
Writing for the Conversation, Prof. Dr. Michael Butter of the University of Tübingen reports that "there is not a single sentence in the document that indicates the CIA intended to weaponise, let alone introduce the term 'conspiracy theory' to disqualify criticism. In fact, 'conspiracy theory' in the singular is never used in the document. 'Conspiracy theories' in the plural is only used once." Butter then cites a sentence from the second paragraph of the Warren Report that reads as follows:
"Conspiracy theories have frequently thrown suspicion on our organisation, for example, by falsely alleging that Lee Harvey Oswald worked for us."
The words "conspiracy" and "theory" have been in use for centuries. By searching Google Books from the 1800s to 2019, we can see that the term "conspiracy theory" first started to appear in the 1870s, and then took off in popularity during the 20th century. According to etymoline.com, the term "conspiracy theory" was used from the 19th century in a non-pejorative sense.