This method of propaganda was not always as widespread as it is today. The phrase was not "created" by the CIA, but it was in fact weaponized by them in the 1960s after the assassination of John F. Kennedy with the express purpose of shutting down rational debate.
CIA memo 1035-960, circulated within the CIA in 1967 and exposed through a freedom of information act request by The New York Times in 1976, outlines strategies the agency would use to shut down critics of the Warren Commission Report. Specifically, they suggested the accusation of "conspiracy" with negative connotations attached, predominantly in mainstream books and articles. This was indeed done through the CIA's many puppets in the media, and the concept of "conspiracy theory" as a pejorative was born.
Through the use of straw man arguments, red herring fallacies and sophistry, the incredible scale of evidence (exposed by investigators like New Orleans District Attorney Jim Garrison) suggesting the Warren Commission was either corrupt or ignorant in its findings was buried in a flurry of hatchet jobs and hit pieces. And this was the goal, of course; to attack the messenger and silence the truth without having to go through the ugly process of directly confronting the truth.