Encouragingly, ABC News has produced a documentary that is disturbing for the right reasons. "The Supreme Court of the United States," though slow to get started, brings into focus some of the unwieldy great issues the nine justices will face in the months and years ahead, at a time when the court itself has reached, as correspondent Marshall Frady says, "a moment of significant, perhaps historic, transition." Which is putting it gently.

The hour-long "Close-Up" report, at 10 tonight on Channel 7, includes glancing interviews with Justices William Rehnquist and Harry Blackmun, the only two who would participate. Rehnquist demanded and got special treatment. As Frady explains, "We agreed to let him review his responses used in this broadcast because of the sensitivity of a Supreme Court justice commenting on current affairs."

These justices always seem to come with strings attached. When Chief Justice Warren Burger, tireless media hater, agreed to appear on "Nightline" earlier this year, it was with the stipulation that only prison reform be discussed. The result was a tediously repetitious hour.

And yet the brief moments of talk among the two justices and Harvard law professor Arthur Miller seen on tonight's documentary were probably worth the trouble it took to get them.

For instance, from the way Rehnquist answers certain questions, if not precisely from the words he uses, one may get the feeling that he looks upon the Bill of Rights as an obstacle to be circumvented, something a trifle pesky. Rehnquist does not agree that civil liberties have been chipped away by decisions of the Burger Court. Blackmun, anticipating such volatile issues as school prayer, says, when asked about the condition of the "wall" between church and state, "One can certainly say it has been damaged here and there."

There is powerful material contained within the program's survey of pending major cases, especially those that involve religious or pseudo-religious matters. Looking into the faces of mindless, yammering zealots who think the country and its schools are theirs, one gets a dispiriting jolt of de'ja vu. Where have we seen those faces before? Of course -- it was in newsreels during the days of violent opposition to school integration. The dogma changes somewhat, the hate is masked in demonstrative piety (even cries of "Amen!"), but it's really the same ugly mind set all over again.

Other cases discussed include those of high school students in Arkansas who are forced to take breathalyzer, blood and urine tests to determine if they have been ingesting drugs, and cases that are brought about by the confounding complications of new technology, principally the artificial prolongation of human life. The mother of a baby who had been kept alive by a respirator and suffered apparently debilitating brain damage in the process says, "We chose to just let Christopher die a dignified, a loving death."

Most wrenchingly, a man who was returned to consciousness, or a state approximating consciousness, after 20 months in a coma, and barely able to function in a human state, weeps when his wife describes his overwhelming impairments to a reporter. Not dead, but only nominally alive, he is, says the Rev. John Paris of Holy Cross College, "trapped in a body that is totally nonresponsive." To free him would legally be called murder.

There are many flaws in the program. No truly outspoken critics of the Burger Court or the Reagan administration are heard; it's never communicated that some thoughtful, respectable people are outraged by what has happened to the court and what may yet happen if Reagan gets to make a few more appointments. Instead of plunging into the subjects at hand -- enormous and complex matters -- Frady and producer Ann Garfield Black diddle around with a circuitous introduction about immigrants arriving on Our Shores, scenes of which are accompanied by hokey-soapy musical hype (artful touches of Philip Glass are used much later).

Perhaps it was thought that the best way to lure viewers into a serious documentary would be to butter them up with some of ABC's weary flag-waving. Why not a flashback to a couple of U.S. victories at the Summer Olympic Games? It's been five or 10 minutes since ABC dredged those up.

Visually, the program includes large amounts of diversionary gingerbread (shots of trucks zooming into Arkadelphia, Ark., for example) and much prowling of the empty court chamber by a camera. It's nice they were allowed to get in there with a camera, but once you've seen an empty chamber, you've pretty much seen an empty chamber.

This is not an empty hour, however -- just one that's not quite as full as it should have been. It still has plenty of material to give one pause, concern and even shudders.