YOU WOULD THINK that the administration which certified human rights progress in El Salvador would have no trouble at all doing the same for Chile.

But there is an excellent prospect that they will not be able to give Gen. Agosto Pinochet the good conduct medal -- not because there is a sharp difference of opinion, even within the State Department, over the general's behavior toward his fellow Chileans, but because of the ghost of Orlando Letelier.

Alas, for those who favor fascists, the bill which authorizes resumption of military aid to Chile depends not only on certifiable human rights advances but on evidence that Pinochet is exhausting "all legal means" to help solve the murder of Letelier, the Chilean exile who, with Ronnie Moffitt, was killed in a car-bombing in Washington in September 1976.

Reagan is apparently ready to let other Latin American governments know that anything goes as long as they are not red. With the certification of Chile, Reagan would be telling the new dictators in Guatemala, for instance, that we can forgive anything -- even murder in our streets by their hired thugs -- so long as it is done in the name of anti-communism.

But Letelier, from the grave, can do what no witness of steady human rights deterioration in Santiago can accomplish -- and that is stop certification in its tracks.

The publication of new letters by Michael Townley, the chief of the Letelier-Moffitt assassination team, sent a wave of panic through the State Department. Townley, the American button man, revealed that Gen. Pinochet -- who is regarded so warmly by U.N. Ambassador Jeane Kirkpatrick, Assistant Secretary for Inter-American Affairs Thomas O. Enders and other officials of a government which has taken its stand against international terrorism (jump starts here) Townley is the American button man who revealed that Pinochet may actually have met to congratulate the assailants of Bernardo Leigh, another Chilean exile leader who, with his wife, was gunned down in the streets of Rome.

Enders made an emergency trip to Santiago earlier this month to plead for some show of cooperation in the Letelier murder.

As usual, it was no dice.

Pinochet does not dare to extradite Gen. Manuel Contreras, former chief of the Chilean secret police (DINA), and two high-ranking confederates who were indicted by a federal grand jury in the murder. He obviously has no intention of bringing any of them to trial.

The current showing of "Missing," a Costa- Gavras docu-drama which charges U.S. embassy complicity in the murder of an American during the Pinochet coup, has not assisted greatly in creating a climate for certification. What is going to make it immeasurably worse is a book called "Labyrinth," by Taylor Branch and Eugene Propper, the young U.S. attorney who stalked Letelier's killers and who, with the help of the FBI, ran them to earth.

But the chief resistance to State's plans to wash away Chile's sins comes from within the administration. The Justice Department is enormously proud of its role in bringing in the terrorists. Never mind that the guilty convictions of three of the thugs were overturned. The successful manhunt was one of Justice's finest hours. Against all left-wing expectation, the FBI and the 29-year-old prosecutor moved against a conspiracy of the right.

When the deputy chief of the major crimes division, E. Lawrence Barcella, who was deeply involved in the chase, was asked recently how well Chile had cooperated in the Letelier investigation, he said succinctly, "Chile hasn't done spit."

This kind of talk sent a shudder through Foggy Bottom where, for all sorts of reason, many would like to think the best about Pinochet. The Justice Department, on being asked for information, sent over a long letter in which the noncooperation of the Pinochet government was crushingly detailed. The State Department then requested a meeting with Justice to iron out their differences. It occurred in mid-March.

Rudolph W. Giuliani, associate attorney general, was the senior man present -- State was represented at the deputy assistant secretary level -- and he was adamant. The facts were the facts. He told the disappointed State people that their quarrel was not with the Justice Department but with Congress, which had passed a law requiring Pinochet to come across on Letelier.

"Justice has passed the word that it cannot control its professionals in the Letelier matter -- they'll be up the Hill like a shot to testify about noncooperation," reports Tom Harkin, a human rights leader in the House.

So the bureaucrats, of all people, are staving off another foreign policy disaster. Some people in State would have liked to fight it out on human rights grounds. They think they could have won.

"It is the greatest human rights victory of this administration," said one State Department official, who, of course, could not have his name used