IT SOUNDED RATHER AUDACIOUS from the start: with all those Democrats jockeying for federal jobs, the President was going to retain a Republican, Jack M. Eckerd, as head of the General Services Administration because the job ought to be non-political. We would have applauded - but there wasn't time. Within four days Mr. Eckerd had been torpedoed by - what else? - politics.

Mr. Eckerd, it seems, thought the White House had agreed to let him have the deputy administrator of his choice. But on the day his retention was announced, President Carter told him that White House aide Hamilton Jordan was committed to giving the number two job to Robert T. Griffin, a longtime GSA official and friend of House Speaker Thomas P. O'Neill Jr. After thinking this over, Mr. Eckerd decided his position had become "untenable." He resigned.

Apart from the awkward sequence of events, there is nothing outrageous or even unusual here. To lure good people into top jobs, a President often has to promise them wide latitude in staffing their agencies - and then somehow reconcile that with many other commitments and political debts. Appointees such as HEW Secrtary Joseph Califano and Secretary of State Cyrus R. Vance, who are more politically experienced than Mr. Eckerd, have had to move quickly to install their own choices in subcabinet posts.

Nor is it surprising that the White House felt obliged to mollify Mr. O'Neill. The Speaker had been more than somewhat irked by Mr. Carter's first two appointments from Massachusetts, Republican Elliot Richardson as an ambassador-at-large and former Republican Evan Dobelle as chief of protocol. Both are seen as possible rivals of Mr. O'Neill's son in a future Bay State gubernatorial race. After those two affronts to the Speaker, the White House obviously seized a chance to recoup by elevating Mr. Griffin - who, onthe merits, appears to be well qualified.

What is unfortunate about all this is that the top jobs at GSA have once again become embroiled in patronage, and congressional patronage at that. Under Mr. Eckerd's management, the agency was just recuperating from the era in which it often seemed to be a wholly-owned subsidiary of the Pennsylvania GOP establishment presided over by former Senate Minority Leader Hugh Scott. The selection of Mr. Griffin partisanship at GSA. After last week's fiasco, however, the White House will have to try that much harder to find a new administrator - presumably a Democrat - who will be as non-partisan and effective as Mr. Eckerd has been.