This was originally "Counter Intelligence Programme," an FBI operation targeting US domestic dissent in the 1970's.
The methods of cointelpro include placing agent provocateurs into targeted organizations, false allegations of wrongdoing, planting false evidence, setting up fake organizations for fomenting discord within a movement and many other modes of harassment and disruption.
The QFS sees much of the New Age movement as 'cosmic cointelpro,' aimed at propagating plausible lies for misleading those who are no longer content with the answers of standard religion. The 'space brothers are here to save us' is an example of such a meme.
Essentially, cointelpro is any covert or underhanded activity aimed at destroying movements or ideas the power structure finds threatening while maintaining deniability. The extreme factionalization of the UFO research community is an example of the results of cointelpro.
See Cosmic Spam and other articles at the Cassiopaea web site.