NO ONE CAN accuse the Pentagon of shooting its wounded.

This week, one of its favorite contractors got into a little jam with the law. General Dynamics, the country's third-largest weapons maker, and three of its officers, were indicted for fraud, specifically for a little sleight of hand with cost overruns, moving them around in their books to conceal their existence.

One of the three named, James M. Beggs, former General Dynamics vice president and board member, is currently administrator of the National Aeronautics and Space Administration.

Navy Secretary John F. Lehman, Jr., understanding that his department is officially at war with fraud, leapt up and fired a suspension of indefinite duration at General Dynamics. That meant that General Dynamics would get no new contracts until the matter was resolved.

That was on Tuesday.

By Wednesday, the Pentagon decided that General Dynamics had suffered enough.

Secretary Lehman didn't lift the suspension. He just did the next best thing. He extended the period in which he would take bids on a nuclear- powered attack submarine which only Newport News and General Dynamics seem to be able to produce.

Said Lehman, in one of the most confusing declarations ever to come out of the Reagan administration, "This is an action to protect the public interest; that is, competition and therefore lower prices in shipbuilding. It would be foolish of us to award a soul-source contract just to spite another contractor."

The phrase "to spite another contractor" leaps out because it goes to the heart of the problem. The secretary of the Navy thinks like a defense contractor, not a public servant ready to smite raiders of the public treasury. He thinks it is more important to build weapons than to quibble over who is building them. A little matter of dealing with a company that is alleged to have robbed the government of $3.2 million by concealing over-runs in other accounts, in his eyes, does not disqualify it from doing more business with Uncle Sam.

No defense contractor who has been listening to Defense Secretary Caspar Weinberger would have reason to think that any moral, legal or human consideration begins to compare in urgency with the defense buildup.

Defense contractors, at least the major ones who turn out the big-ticket items, understand that no matter what indictments the Justice Department task force on General Dynamics may bring in, the Pentagon will go on protecting and preserving the people who fleece it.

Suspension is a sometime thing at the Pentagon anyway. It is a kind of ritualized moral indignation that neither side takes seriously. Recently, when called upon to disapprove of General Electric, the Pentagon went through the drill. The suspension was two days old when the Pentagon suffered a new-weapons attack; it lifted the suspension, awarded GE a handsome contract and slid the suspension back into place.

Rep. John Dingell (D-Mich.), the demon investigator who put General Dynamics executives on the griddle for charging taxpayers for kennel fees and country club dues, says that until the Pentagon takes actions that cause pain to its greedy suppliers, the piracy will go on.

Dingell thinks that if an errant contractor who has the use of a government facility is denied that facility as punishment, with resultant drop in profits, the light might dawn.

The Pentagon has no wish to inflict pain on its peddlers. They have a close, warm, intimate relationship, which drearinesses like monitoring, disciplining and auditing could only blight. The Pentagon thinks its duty to the public begins and ends with blanketing it in steel. It has to spend more than a billion dollars a day to stay even with Congressional largesse. Only a few people like whistle-blower Ernie Fitzgerald have time to think about cutting cost.

The indictment of a high official of the Reagan administration on allegations of cooking the books is, Dingell thinks, wholesome in that it may encourage second thoughts in the boardroom. The president huffed that the alleged offense was old and had not enriched Beggs personally.

That represents a slight lowering of the ethical threshold. Once, indictment was cause for resignation. That was established in the matter of Raymond Donovan, former secretary of labor. But Beggs has been allowed to take a leave of absence from NASA. Apparently, only conviction is now considered grave enough to warrant removal from high office.

Perhaps we should be grateful that the Justice Department, even under Ed Meese, is still operating on the basis that defrauding the government is wrong, even if one of the two defense contractors who can make a nuclear attack submarine is doing it.