In order to make sure as to what the whole issue is (or I think it is), I will quote excerpts from the Wikipedia. My own text/comments will be in red.
COINTELPRO encompassed disruption and sabotage of the Socialist Workers Party (1961), the Ku Klux Klan (1964), the Nation of Islam, the Black Panther Party (1967), and the entire New Left social/political movement, which included antiwar, community, and religious groups (1968). A later investigation by the Senate's Church Committee (see below) stated that "COINTELPRO began in 1956, in part because of frustration with Supreme Court rulings limiting the Government's power to proceed overtly against dissident groups ..." Official congressional committees and several court cases have concluded that COINTELPRO operations against communist and socialist groups exceeded statutory limits on FBI activity and violated constitutional guarantees of freedom of speech and association.
The program was successfully kept secret until 1971, when the Citizens' Commission to Investigate the FBI burgled an FBI field office in Media, Pennsylvania, took several dossiers, and exposed the program by passing this material to news agencies. Many news organizations initially refused to publish the information. Within the year, Director J. Edgar Hoover declared that the centralized COINTELPRO was over, and that all future counterintelligence operations would be handled on a case-by-case basis.
Additional documents were revealed in the course of separate lawsuits filed against the FBI by NBC correspondent Carl Stern, the Socialist Workers Party, and a number of other groups. In 1976 the Select Committee to Study Governmental Operations with Respect to Intelligence Activities of the United States Senate, commonly referred to as the "Church Committee" for its chairman, Senator Frank Church of Idaho, launched a major investigation of the FBI and COINTELPRO. Journalists and historians speculate that the government has not released many dossier and documents related to the program. Many released documents have been partly, or entirely, redacted.
The Final Report of the Select Committee castigated conduct of the intelligence community in its domestic operations (including COINTELPRO) in no uncertain terms:
The Committee finds that the domestic activities of the intelligence community at times violated specific statutory prohibitions and infringed the constitutional rights of American citizens. The legal questions involved in intelligence programs were often not considered. On other occasions, they were intentionally disregarded in the belief that because the programs served the "national security" the law did not apply. While intelligence officers on occasion failed to disclose to their superiors programs which were illegal or of questionable legality, the Committee finds that the most serious breaches of duty were those of senior officials, who were responsible for controlling intelligence activities and generally failed to assure compliance with the law. Many of the techniques used would be intolerable in a democratic society even if all of the targets had been involved in violent activity, but COINTELPRO went far beyond that ... the Bureau conducted a sophisticated vigilante operation aimed squarely at preventing the exercise ofFirst Amendment rights of speech and association, on the theory that preventing the growth of dangerous groups and the propagation of dangerous ideas would protect the national security and deter violence. ????
And now we come to the Chomskian suggestion that the removal of Nixon from office served to keep the worse aspects of COINTELPRO secret
?.. In a 1996 'Big Idea' interview with BBC journalist Andrew Marr, Noam Chomsky suggests that the revelation of COINTELPRO was actually vastly more significant than Watergate, exposure of which happened at exactly the same time. While Chomsky doesn't allege a conspiracy per se, he seems to imply that the apparently convenient timing might suggest that President Nixon could have been sacrificed to drown out media interest in COINTELPRO or that at the very least, the fact that the full extent of the COINTELPRO programme remains relatively unknown is proof that the press has done a poor job in investigating the FBI's activities even once they have been admitted. It was later revealed that the secret Deep Throat source who tipped off Washington Post journalists Bob Woodward and Carl Bernstein to the Watergate break-in source was FBI Associate Director Mark Felt for reasons which, according to Chomsky, have never been conclusively explained ?..
My overall understanding is that the COINTELPRO program was a criminal enterprise by people who should have been sent to gaol.