A South African judge today ordered police not to assault black political prisoners after a state-employed doctor testified that there appeared to be a "systematic pattern of abuse" of blacks detained under the emergency decree issued two months ago.

While the doctor, Wendy Orr, was making her disclosures in an eastern Cape Province court, two other cases revealed the hostile reaction of the authorities to criticism of police action in the region, which has been the worst affected by South Africa's 14 months of racial unrest.

In one case, a white woman provincial councillor is being charged with criminal libel for suggesting that an officer at a police station, where she witnessed a manacled black prisoner being whipped, had been drinking.

In the other case, the editor of a local newspaper is charged with a reporter for publishing a report, which the police deny, that an antiriot unit dispersed a black crowd with tear gas and whips.

Orr was one of 44 persons who asked the provincial Supreme Court in Port Elizabeth for an order restraining the police from assaulting black political prisoners in the eastern Cape Province region, which has been the scene of continuous unrest since January and where hundreds of black activists have been detained under the emergency regulations.

Orr said she had seen "overwhelming" evidence during her work in Port Elizabeth prisons that black political prisoners were being "systematically assaulted and abused."

She said she had been ordered not to record cases of alleged assault in the official medical registers, but had noted elsewhere that she had examined 286 prisoners who complained of having been assaulted between July 22 and Sept. 16. Of these, 153 had injuries that could not have been inflicted lawfully, Orr said.

The police did not oppose the request, and Judge J.P.G. Eksteen granted the order of restraint, which he said should be read to all detainees in the Port Elizabeth area.

Fifty Christian leaders of several denominations issued a joint theological document in Johannesburg today stating that the church would have to "confront the apartheid regime" and become involved in civil disobedience.

The strongly worded document declared that the church could not "collaborate with tyranny" or do anything that appeared to give legitimacy to a "morally illegitimate regime."

Molly Blackburn, a liberal member of the Cape Provincial Council and a prominent civil rights campaigner, appeared in a Port Elizabeth magistrate's court today charged with criminal libel for suggesting during a visit to a police station March 21 that an officer, Lt. John Fouche, was drunk and unfit to perform his duties.

Fouche said he felt insulted and injured by Blackburn's accusation, which he said was untrue. The case is continuing.

J.C. Viviers, the editor of Port Elizabeth's leading newspaper, the Eastern Province Herald, and a reporter, Juliette Saunders, appeared in court today accused of publishing a false report stating that police used whips and tear gas to disperse a crowd of black demonstrators at the funeral of a black unrest victim last November. Police witnesses have testified that tear gas and whips were not used that day.