The Supreme Court, acting in one of the most highly publicized murder cases of the 1970s, yesterday reinstated the conviction of Jeffrey R. MacDonald, the former Green Beret doctor accused of murdering his pregnant wife and two children at Fort Bragg, N.C., in 1970.

By a 6-to-3 vote, the justices overruled a lower court decision that had freed MacDonald because of excessive delay in bringing him to trial between 1970 and 1979. Chief Justice Warren E. Burger, writing for the court, said that because MacDonald was not formally charged or under arrest during much of that period, he was not protected by the constitutional right to a speedy trial.

The FBI arrested MacDonald, 38, at his Huntington Beach, Calif., apartment within an hour of the ruling and returned him to the prison he left after the lower court decision in 1980. MacDonald, a Princeton graduate whose case attracted an emotional following on both sides, faces three consecutive life terms.

He still has a chance to win his freedom on other legal issues.

MacDonald's wife, Colette, 24, and his two children, Kimberly, 6, and Kristen, 3, were stabbed and bludgeoned to death in February, 1970, in their home on the military base. MacDonald attributed the crime to a Charles Manson-style hippie cult, which he said invaded the home chanting, "Acid is groovy," slaughtered his family, beat and stabbed him and scrawled "Pig" in blood on a headboard in the master bedroom.

The Army accused MacDonald of the crime shortly thereafter but dropped the charges a few months later. Heavy Washington lobbying by MacDonald's father-in-law, Alfred Kassab, influenced the reopening of the case by the Justice Department, which won an indictment in 1975, and a conviction--based on pajama threads and other physical evidence--in 1979.

MacDonald sought exoneration through a private investigation and his own public relations campaign, financed by numerous friends who believed in his innocence. In July, 1980, the Richmond-based 4th Circuit U.S. Court of Appeals freed him on the speedy trial issue.

Burger said yesterday that the lower court mistakenly clocked the delay from the time of the first Army charges against MacDonald in 1970 to the trial in 1979. In fact, he said MacDonald was a free man, facing no criminal accusations, after the Army dropped the charges. He noted, however, that the court was right that MacDonald's life was disrupted by publicity and the ongoing investigation during this period.

But "with no charges outstanding, personal liberty is certainly not impaired to the same degree as it is after arrest while charges are pending," Burger wrote. " . . . The speedy trial guarantee is designed to minimize the possibility of lengthy incarceration prior to trial, to reduce the lesser, but nevertheless substantial, impairment of liberty imposed on an accused while released on bail, and to shorten the disruption of life caused by arrest and the presence of unresolved criminal charges.

" . . . Once the charges instituted by the Army were dismissed, MacDonald was legally and constitutionally in the same posture as though no charges had been made."

The lower court ruled that the delay might have denied MacDonald a fair trial by eroding memories of witnesses. Burger said that question was a separate one, unrelated to the speedy trial issue, which the lower court would have to reconsider.

Justice John Paul Stevens agreed with the ruling but issued a separate statement clarifying his reasons. Justices Thurgood Marshall, William J. Brennan and Harry A. Blackmun dissented, saying Burger's opinion "presents a serious potential for abuse" by prosecutors.

The ruling underscored the Burger court's tendency to require evidence of actual unfairness--not just the potential for unfairness--before throwing out a conviction.

Kassab, MacDonald's father-in-law, said he was relieved that his 12-year campaign had succeeded, adding, "I hope this gets him back in jail as soon as possible."

Brian Murtagh, the prosecutor on the case for nearly a decade, said the FBI had been watching MacDonald each morning the court might have ruled during the past few weeks to make the arrest. He said he was concerned MacDonald might flee.

"They gave him time to shave," a friend said of MacDonald's arrest, after which he was taken to the Terminal Island (Calif.) federal prison.

From behind bars, MacDonald sent word he would have no comment.