IN STEPPING down as head of the Arms Control and Disarmament Agency and as chief strategic-arms negotiator, Paul Warnke leaves both enterprises in better condition than they were in when he come aboard. ACDA has won the clear voice in helping the broad arms-control policy that those who set up the agency intended and that the public interest requires. The SALT talks are reported to be on the verge of producing an agreement. These are substantial achievements in a field where achievements of any sort are hard to come by.

As part of the personal harassment to which he has been regularly subjected, it is being said of Mr. Warnke's departure that he was pushed - that President Carter, in effect, has repudiated him. As it happens, that is false. He is leaving at a moment when, given the uncertain political climate surrounding SALT, it may help the administration to have a less controversial SALT negotiator. But he is leaving by prearrangement for reasons of his own. Far from repudiating him, the president is paying him the ultimate tribute of moving ahead to complete and then present the very treaty he negotiated. Often hysterically, his critics have tried to paint the cool Mr. Warnke - again, falsely - as some sort of soft unilateral disarmer. They have had neither the grace to concede he was conducting not his own policy but the administration's, nor the stomach to attack President Carter head on.

As SALT negotiator Mr. Warnke is being succeeded by his deputy, Ralph Earle II, an experienced hand without either Mr. Warnke's high political profile or his high prestige. As head of ACDA, the president has nominated retired Lt. Gen. George M. Seignious II, who used to be, among other things, the Pentagon's chief arms salesman. Now he is to head an agency that was given separate life precisely to institutionalize a non-military approach to national security. We are sure that, for one, Sen. Henry M. Jackson (D-Wash.), a foe of Mr. Warnke's, will want to assure himself in the confirmation hearings that the general is the right man for the job.