THE JUSTICE DEPARTMENT had come to regard the Richard Helms affair with all the warmth that a ship's captain reserves for a school of barnacles firmly attached to a vessel's hull: a nuisance--if a major one--that would pop into public view every so often, only to submerge once again below the Koreagate and Bert Lance headlines.

Just how trying a dilemma the Helms case presented to Atty. Gen. Griffin B. Bell and company became apparent last week. Justice clumsily announced that the department had seen fit to work out a very special deal with the former head of the Central Intelligence Agency (CIA). As Helms and his renowned attorney Edward Bennett Williams walked into a federal district courtroom last Monday to file a nolo contendere plea to two misdemeanor counts against Helms for failing to testify fully before a Senate committee four years ago, Bell at that moment was informing President Carter of his "just and fair disposition" of the case. Confronted with a virtual fait accompli, Carter hastily gave Bell his consent, and the four-year-old Helms investigation came to an abrupt end.

The prospect of handling down an unprecedented indictment of a former CIA director on serious perjury charges daunted the Justice Department from the very beginning in 1973 when Helms lied about CIA involvement in plots to secretly deliver funds in 1970 to the opponents of the late Chilean president Salvador Allende Gossens. Once on the witness stand, there was no telling how many intelligence secrets a desperate Richard Helms might cough up to save his own neck. Conversely, Justice officials and, in particular, the Carter administration acknowledged the need to hold Helms accountable for his transgressions while under oath; the post-Watergate ethos and Carter's own promises for an "open Administration" still pervade Washington.

Bell and the Criminal Division of Justice settled for a compromise, hoping to provoke a storm that would blow over with the passing of a few weeks. They persuaded Helms to enter a plea of no contest to significantly reduced charges, thereby officially recording Helm's guilt without risking the disclosure of information in an open courtroom that could damage the country's national security interests. Or so the argument goes.

BUT A FEW unusual circumstances surrounded the disclosure of the resolution of the troublesome case. For one thing, Justice Department officials, in a departure from normal procedure, failed to notify reporters of Helms's day in court until after the former CIA director had entered the courtroom. Bell's post-mortems on the Helms affair informed reporters that he had first discussed the matter of a Helms plea bargain back on July 25 in an Oval Office meeting with Carter and assorted high-level administration officials. This statement is directly at odds with Carter's late September assertion that his knowledge of the case was confined to press reports he had scanned. And Benjamin Civiletti, the head of the Criminal Division in Justice, who figured prominently in the negotiations with Helms and his attorney, disclosed that, in yet another unorthodox step, Justice had actually initiated the backroom talks with the former CIA chief, hoping to reach the very arrangement they announced last week.

The steady unearthing of such details has aroused some unfocused doubts as to the credibility of the reasons the Carter administration officials advanced for their peculiar handling of the Helms affair. These understandable misgivings are only reinforced by closely examining the arguments mustered in defense of the final resolution. That Richard Helms lied through his teeth before the Senate Foreign Relations Committee four years ago cannot now be challenged; subsequent investigations by Congressional panels and the press established the CIA's complicity in funnelling more than $8 million to Allende's opponents in the early years of this decade.

Helms stood on very shaky legal ground as well. The oath he took as CIA director to protect the nation's intelligence secrets did not even begin to excuse his perjury before Congress. He need only have declined to testify on matters involving a conflict of these two oaths when he appeared on Capitol Hill; instead, Helms consciously chose to deceive the senators.

PERHAPS THE STRONGEST argument advanced against a Helms trial drew heavily on the complications resulting from efforts by Helms' counsel to subpoena sensitive national security documents to use in the courtroom proceedings, a move that might have forced prosecutors to dismiss the case in midtrial. This contention, however, does not bear up under close scrutiny. All requested materials of this nature would have been referred directly to the trial judge, who would have determined each document's relevance. Handing over this weighty responsibility to a presumably independent judge unhindered by political considerations would have proven to be the wisest move, especially in light of federal Judge Barrington D. Parker's no-nonsense rebuke of Helms during the sentencing proceedings last Friday. Government prosecutors might well have moved to dismiss the case as feared, but the mere fact of sending the case to the branch of government in which it properly belongs would have avoided the cynicism that greeted the Helms plea in many quarters last week.

The critical right of Congress to exercise meaningful oversight of the nation's intelligence community has sustained a serious--albeit hardly fatal--blow in the wake of the administration's decision on Helms, and only a very tenuous silver lining could be discerned as the air cleared in Washington. As part of the bargain with Justice Department officials, Helms agreed to testify fully in any subsequent investigations pertaining to the entire CIA episode in Allende's Chile.

THE ONGOING PROBE of possible perjury committed by two International Telephone and Telegraph Company (ITT) executives--chief executive Harold S. Geneen and senior vice president Edward J. Gerrity--still awaits action by Justice, and a complete account by Helms as government witness rather than defendant might yet salvage a bit of legitimacy for the leniency recently shown him. Given the suspended sentence meted out to Helms and his retention of pension rights despite his no contest plea, such cooperation with the government would furnish some limited evidence that Helms indeed recognizes the gravity of his misdeeds. Otherwise, the nation will be left with one lingering image of Richard Helms, that of a jaunty one-time Nixon hatchet man who views his nolo contendere cop-out as a "badge of honor," not the scarlet letter of "disgrace and shame" Judge Parker so eloquently described.