SECRETARY OF LABOR Raymond Donovan has at last resigned, a thing that he might better have done in October when he was indicted. He was hardly an asset to the administration, and a man with a clearer sense of propriety would have departed instantly. But Mr. Donovan clung to his office and his title in the hope -- misplaced, as it turns out -- that the court in New York would dismiss the indictment.

Mr. Reagan has sent Mr. Donovan off with a letter warmly expressing "my friendship and gratitude for the years of service you have given to this administration." Mr. Reagan has treated Mr. Donovan a good deal better than Mr. Donovan, dragging the administration through one embarrassment after another, has served his patron. The whole episode shows the president at his most generous and tolerant.

But perhaps there is a little more here than generosity alone. A president is often tempted to dismiss all ethical questions involving his appointees as nothing more than veiled political attacks on himself. That response is one of the few things that the Reagan White House has in common with the Carter White House. But if that reaction is understandable on the part of a president, it is also a point of vulnerability. And Mr. Donovan is accused of a breach not only of ethical standards but of the criminal laws.

Ever since his original confirmation hearings four years ago, he has been pursued by the same cluster of doubts and suspicions involving his associations and his activities in the construction business. An FBI report delivered to Mr. Reagan's transition team in January 1981 said that the bureau had no evidence of criminal behavior on Mr. Donovan's part but reported information that he had ties "with known La Cosa Nostra figures." When that report finally reached the Senate Labor Committee more than a year later, the chairman, Orrin Hatch, who is no adversary of the administration, suggested that it was time for Mr. Donovan to leave.

The special prosecutor, Leon Silverman, reported later in 1982 that he had found "insufficient credible evidence" of violations of law. But last fall a grand jury in New York concluded that Mr. Silverman had not looked far enough, and it indicted Mr. Donovan. He took a leave of absence and asked the court to throw out the indictment. But the judge has now declined.

What's been going on, meanwhile, at the Labor Department? Not much -- even less than if the secretary's office had been empty for these past four years, since the presence of Mr. Donovan and his recurring troubles were a positive distraction. At this point, Mr. Donovan's overdue departure can only benefit the department and the people whom it is supposed to be serving.