Repudiating the Arms Control and Disarmament Agency and Paul Warnke, its ousted director, President Carter on Sept. 29 quietly signed Presidential Directive 41, ending 15 years of dangerous inattention to the role of civil defense as part of the strategic balance of power.

Carter's approval of the secret directive is given political importance by the White House beyond its pledge for a sizable boost to civil defense. Lobbied hard by Zbigniew Brzezinski, Carter's national security aide, the new plan is also percieved as a vehicle to soften Senate opposition to SALT II, the new strategic arms limitation treaty expected to be signed later this year.

"What is imperative in selling SALT II," one administration official told us, "is to dispel suspicious among Senate skeptics that it points to future weakening of the U.S. strategic position across the board."

Questions about Carter administration defense policies in the post-SALT II period will figure heavily in the Senate treaty debate, certain to be prolonged and bitter. For example, Henry Kissinger - whose views on SALT II could critically influence its fate in the Senate - has confided to key senators that his own position may depend on whether Carter can make a credible case for a strong strategic U.S. posture, including nuclear arms, in the post-SALT era.

Behind PD 41 may be Carter's hope os smoothing the way for SALT II. But considering the long months of study in the Pentagon and National Security Council that preceded its adoption, PD 41 seems less aimed at SALT II than at correcting a grave deficiency in the U.S. strategic posture by raising annual civil-defense spending from less than $100 million to almost $400 million. The SALT II palliatives are far more obvious:

First, the ouster of Paul Warnke, controversial ACDA director and chief U.S. negotiator for SALT II. Clearing Warnke out of ACDA before the Senate gets the new treaty was essential. With Warnke as SALT II salesman, the prospect of the treaty being bought by the two-thirds majority needed for approval would have been negative.

Second, the surreptitious courtship by administration officials of Paul Nitze, probably the most rigorous proponent of U.S. strategic strength. The White House is desperately eager to win Nitze's nod of approval for Warnke's successor. The first serious White House effort to recruit a new ACDA boss who might meet the Nitze test failed when Brent Scowcroft, Brzezinski's predecessor as national security chief under Gerald Ford, turned it down. Retired Army Lt. Gen. George Seignious Jr. is now under consideration.

Third, the president's highly publicized but ambiguous announcement Wednesday that he may be moving toward production of the neutron war-head.

The new civil-defense directive stands on its own feet even though the administration hopes it will have marginal significance in the SALT II debate. Its real importance lies in Carter's recognition that civil defense - population safeguards for survivability against a Soviet nuclear strike - must be counted as a factor in the strategic balance. That policy decision buries dreamlike arguments of the arms-control lobby that nuclear war is unthinkable because both sides know they are mutually vulnerable to attack under what is called Mutual Assured Destruction (MAD).

The MAD theorists have now collided with hard facts made known to Carter by reliable Central Intelligence Agency studies last summer. Annual civil-defense spending in the Soviet Union is at a rate of a leat $2 billion, and more than 100,000 full-time personnel are engaged in civil-defense efforts to minimize the loss of human and industrial resources in case of attack. In the words of the CIA's July analysis of Soviet civil defense, the Soviet government remains convinced that "civil defense contributes to war-fighting and war-survival capabilities."

The president's decision to set up the new Federal Emergency Management Agency (FEMA) for cilvil defense and to give it nearly $2 billion over the next seven years is a commendable to step, in no small part due to the bulldog determination of ex-McGovernite Democrat Bardyle Tirana. With FEMA's birth, Tirana worked himself out of his job as the Defense Department's civil-defense expert, but the legacy he left ses the United States on a new track from which there should be no retreat, whatever happens to SALT II.