When U.S. District Court Judge Thomas R. McMillen returns to the bench in Chicago tomorrow he'll face another decision in a long-pending and hotly debated case: whether to proceed with the trial of a defendant who, doctors agree, faces a real possibility of dropping dead in the courtroom.

The family of Dr. Milton Margoles, 67, who was charged in May 1978 with illegally prescribing diet pills, claims that the government is persecuting him. His son, Perry, an attorney, even has taken the case to the Helsinki Commission as a human rights violation.

Prosecutors in the office of U.S. Attorney Thomas Sullivan will say only that plans are still to take the ailing Margoles to trial with medical equipment standing by.

"Obviously, we don't want someone kneeling over during a trial," said one federal prosecutor. "But we have an obligation to enforce the law. And it's just impossible to have a standing policy on the problem. We have to do it case by case."

Recent bribery cases against former Rep. Otto E. Passman (D-La.) and Rep. Daniel J. Flood (D-Pa.), were delayed because of illnesses caused by the elderly defendants.

In both of these cases, though, the defendants' ailments were considered temporary ones, from which they could be expected to recover. Margoles suffers from a rare hear disease that cannot be cured by his recent surgery, according to his son.

Perry Margoles said that the prosecutors did offer to let the doctor forgo a trial in return for a guilty plea to a felony, an admission of guilt and forfeiture of his license to practice medicine.

But Margoles refused, in part at least because the family considers the pill-pushing indictment just the latest in a government vendetta that goes back more than 20 years.

Margoles' continuing battle with the Justice Department started with a civil tax case in 1957. That soon became a criminal case and eventually led to a conviction on an attempted obstruction of justice charge as well as the tax count.

The doctor served two years in prison.Over the next several years the family mounted a media campaign against the judge in the case. In 1972 President Nixon pardoned Margoles.

In late 1973, Rep. Robert McClory (R-Ill.) introduced a private bill to reimburse Margoles for the interest and penalties he paid in the tax case. Shortly after a hearing on the bill in the fall of 1974, according to Perry Margoles, "our nightmare started all over again."

The result, after a 17-month investigation by undercover drug agents, was a 37-count indictment. Another result, according to Perry Margoles, was his father's serious heart illness.

The younger Margoles is particularly upset about a July 1978 hearing in which he said federal prosecutors ignored testimony from their own doctors that the defendant was seriously ill.

The consulting physician, Dr. Gerry A. Smyth, said "there is a risk that placing Dr. Milton Margoles in criminal trial might result in his sudden death . . . This risk exists regardless of the length of any such trial or trial sessions."

Even the presence of medical equipment and personnel at the courtroom could not assure that Margoles' life could be saved if the stress of trial triggered an outbreak of irregular heartbeat, known as ventricular tachychardia, Smyth said.

The government presented an investigator at the hearing, who said he had noticed no stress in Margoles when a search warrant was issued the year before. "The government deliberately misrepresented a life-and-death issue," Perry Margoles said.

Judge McMillen set a trial date for last year, but it has been postponed by Margoles' heart surgery. The upcoming court appearance will determine if the defendant has recovered enough to face the charges in court.

Joan Safford, the assistant U.S. attorney now handling the case, acknowledged that the Chicago federal prosecutor's office has dropped other charges because the defendant was too ill. The current position in the Margoles case, however, "is to proceed at such time as the defendant is fit to stand trial," she said.