FOR THE S&L financier Charles H. Keating Jr., the decision in the Lincoln case is a stunning defeat. For the public, the decision is an unprecedented description of the looting -- the term is the judge's -- of a big S&L.

Mr. Keating is the chairman of the Arizona real estate firm that owned Lincoln Savings and Loan, seized last year by the federal regulators on grounds that it was being run unsafely. In a counterattack, Mr. Keating brought suit to force the authorities to return control of Lincoln to him. The judge who heard the case, Stanley Sporkin, is a former chief of enforcement of the Securities and Exchange Commission and a man who knows a great deal about financial manipulation. After hearings over six months, the judge has now found that the regulators were justified in every respect. He outlines a succession of methods by which Mr. Keating's parent company plundered the S&L -- at the ultimate cost to the taxpayer, since the S&L's deposits were insured by the federal government.

But Judge Sporkin goes further, taking the S&L scandal into new territory that, he believes, requires careful public scrutiny. Until now the blame for the enormous losses has chiefly been laid on public officials -- slack and intimidated regulators, interfering congressmen, a Reagan White House desperately trying to keep the subject out of sight until after the last election. Now Judge Sporkin asks pointedly about the responsibilities of the private sector.

He suggests that in a private enterprise system, in a time of deregulation, the duty to prevent this kind of abuse does not lie entirely with public officials. Whatever Mr. Keating did, he did with the active assistance of platoons of highly skilled lawyers and accountants. All of the intricate maneuverings that he describes were made to have an "aura of legality" about them, Judge Sporkin observes. Mr. Keating testified repeatedly that he surrounded himself with legal and accounting talent to ensure that every deal was legal. The judge then asks the deadly question: "Where were these professionals, a number of whom are now asserting their rights under the Fifth Amendment, when these clearly improper transactions were being consummated?"

Judge Sporkin's decision is a disaster for Mr. Keating not only because it rebuffs him in this case but because it also provides a very clear map of the terrain for the various government agencies and grand juries that are now pursuing him. More important, it is a call for reform. Some of it is addressed to Congress. But much of it is a charge to bar associations and accountancy boards to consider this enormous failure of their professional standards to protect both clients and the public.