Administration war hawks claimed these rules prevented the CIA from making deals with bad actors which were necessary for it to do its job. In fact, the regulations in question did nothing of the sort. They still allowed the CIA to deal with anyone it liked. They just required that before initiating dealings with death squad leaders, drug dealers, and assorted murderous thugs, field agents should check with headquarters. Explaining why that was a bad idea is left as an exercise for Dick Cheney.
What brings this up now is the rumors which are swirling around the recent bizarre coup/countercoup action in Venezuela. A sampling can be found at Ethel the Blog, which quotes the usually reliable Stratfor (and also Intel Briefing, of which I know less) to the effect that the CIA was directly involved in the abortive coup. Stratfor in particular spins a bizarre tale of two separate American operations; a State department operation designed to transition back to democratic rule, and a CIA operation piggybacking on top of that, which was designed to put an old-fashioned junta in charge. It was the latter operation, so the story goes, which resulted in the coup leaders' dissolution of the National Assembly --- which, in turn, resulted in the immediate repudiation of the coup leaders by just about everyone else in the country, including the factions of the Army not under their own direct control, which quickly returned Chavez to power.
What lends this bizarre tale credibility, I'm afraid, is that the CIA is well known to have done stuff like this in Latin America in the past --- most notably and shamefully, overthrowing the government of Guatemala over a tax dispute with United Fruit (the Chiquita banana people), ushering in a succession of incredibly brutal dictatorships. It was, in fact, subsequent CIA dealings with an official in one of those Guatemalan dictatorships which lead to the imposition of the 1995 rules on accountability in thugs, after that official was found to be directly implicated in the murder of one American citizen and the spouse of another.
Getting back to Venezuela, if it was a covert op, it was clearly a failure. Which may be for the best; the coup seemed to be tending towards a military junta, and the economic record of those is ambiguous at best (the Argentine junta, for instance, started the Falklands war largely to distract the people from its economic failures), while their human rights record is uniformly dreadful.
But beyond that, the failure itself might prompt fans of the black ops to reconsider whether deniability, even at the cost of planning and review, is truly the highest virtue in covert operations...
Update: The New York Times reports hints that U.S. officials may have encouraged the coup plotters. The Washington Post reports that the administration is denying all involvement, and that at least in public, Latin American governments are claiming to believe it.
What's clear from both reports, though, is that the administration was certainly quick to embrace the coup after the fact, despite its manifestly antidemocratic nature, and both reports are clear that other OAS states, which were quick to oppose the coup (despite their distaste for Chavez himself and his policies) are rather dismayed at the American stand.