In one way, their instinct was spot-on: sure enough, the man who revived all the old theories about the Kennedy assassination in his film JFK didn't buy the official version - that the Boeing aircraft broke up as a result of an explosion in a fuel tank. Mr Stone believed that a US Navy missile downed the plane, and the subsequent federal investigation was a smokescreen to cover up the military's deep embarrassment.
The documentary was duly made, but there was one little problem: nobody at ABC believed a word of it. Furthermore, the FBI were furious about the film's existence, and the victims' families made clear the documentary was one more trauma they could do without.
So, at the end of last week, ABC risked giving even more grist to the conspiracy theorists' mill by pulling the documentary off the air. Not only did they say they were not comfortable with Mr Stone's conclusions, they made it clear they had always viewed his work as "entertainment" rather than serious journalism. "Television viewers could find it difficult to distinguish between the two forms, and we decided not to continue development on this project," the network said in a statement.
The controversy over Flight 800 has raged almost from the moment it fell out of the sky two and a half years ago, killing all 230 people on board.
The missile theory was given enormous credence at first, because of jitters about terrorism at the start of the Atlanta Olympics and because of circumstantial evidence picked up in initial news reports. Eyewitnesses said they saw streaks of light shooting up into the sky moments before the explosion. It emerged that a military sea and air exercise was underway nearby. Was it an audacious terrorist attack? Or a regrettable instance of friendly fire?
The partial conclusion of the FBI and the National Transportation Safety Board was nothing so sensational. The 25-year-old plane, on its way from New York to Paris, had succumbed to an explosion in a fuel tank caused by volatile fuel vapours. The FBI dropped the case on the grounds that no crime appears to have been committed.
The missile theory was almost entirely discredited four months after the crash, when Pierre Salinger, erstwhile spokesman for President Kennedy, claimed he was in possession of government documents "proving" there had been a cover-up. The documents turned out to be a hoax circulating on the internet.
A clutch of former military officers have remained attached to the missile theory, and even paid for a full-page advertisement in the New York Times a few weeks ago to publicise their views. None had any immediate comment on ABC's decision to cancel the documentary.