A decision by the San Diego Chapter of the American Civil Liberties Union to represent a group of Ku Klux Klansmen in a law-suit against the marine Corps has provoked a sharp dispute within the civil rights organization.

Officials of the Southern California affiliate, after New York City's the second largest in the ACLU, say they have received hundreds of protesting letters and telephone calls, primarily from within the ACLU. Thirty-five ACLU members here have already resigned and officials expect more.

The local San Diego chapter - one of 28 in the Southern California ACLU - announced last month it planned to take the case of 16 Marines who were transferred from Camp Pendleton near San Diego to bases throughout the country because of their Klan membership.

The ACLU's involvement in this case has raised the heaviest storm of objection from its members since it took the case in the 1960s of George Lincoln Rockwell, former head of the American Nazi Party.

The Klan issue came to a head after a group of black Marines were accused of attacking seven white Marins at Camp Pendelton Nov. 13 in a mistaken effort to break up what they said they thought was a Klu Klux Klan meeting.

Complicating the situation, lawyers from the ACLU's regional affiliate are defending some of the 13 blacks still facing charges, on grounds that the charge they face - the conspiracy to commit assault - is one traditionally opposed by the civil rights organizaiton.

The ACLU attorneys' entrance into the black marines' case has made the Klan issue even more uncomfortable. ACLU attorneys and officials, however, say the two cases are separate and not related and therefore do not appear to pose a conflict of interest.

Michael Pancer, 35, a San Diego attorney and former president of the 1,600-member chapter there, said he volunteered to take the Klansmen's case after they requested ALCU help. Pancer said the Marine Corps' transfer of the Klansmen violated their First Amendment right of free speech and freedom to belong to a political organization.

"We exist to protect those rights," Pancer declared.

The San Diego chapter's decision, however, has not proved popular here, particularly among the large Jewish and black membership in the Southern California affiliate. They wonder how far even an avowed civil rights organization should go in defending groups whose positions it does not support.

At a formal debate in Beverly Hills last week on "Free Speech and the KKK: The ACLU Dilemma," several dozen members paid $10 each to hear Pancer and Samuel Sheats, a judge in the Los Angeles worker's compensation courts.

Pancer, who received the NAACP's Freedom Fighter Award for defending black servicemen in another military case, told the group, "I may disagree with every position the KKK may have - and in fact I do - but we felt that if the Klan was a political organization they had a right to exist."

Pancer said Klan members at the Marine base had passed out leaflets describing themselves as "the white man's NAACP" and expousing non-violent action to protect whites at the sprawling base.

Sheats, a member of the regional ACLU board of directors and past president of the Pasadena NAACP, attacked the San Diego's chapter's stand. "We are dealing with a black and white issue here and we ought to be very careful about that," he said. "Why should we allocate out resources to these guys?"

Sheats said the civil rights group should exercise "critical judgment" in deciding whether to enter a case. He said he does not recommend "that we should redress every wrong."

In an interview, Pancer complained that ACLU opponents of the suit are describing the Klan members as the violent when no charges of violence have been filed or proved.

"In some ways this thing makes you understand better what it was like to be accused of being a Communist in the 1950s," Pancer said.

Nevertheless, the case has raised questions about allocation of the ACLU's resources. Ramona Ripston, executive director of the ACLU's regional affiliate in Los Angeles, doubted whether the Southern California affiliate would have taken the case if it had come up here.

"There was a time when the First Amendment was a given priority, but other amendments like the Fourteenth now are equally important," Ripston said. "I am still not absolutely certain in my mind about this, but there may be a little difference between the Marine Corps and the rest of society, I would say that if there are still a draft we would have an absolute responsibility to see political rights as guaranteed."

The Kalan and black Marine cases have posed some uneasy confrontations between ACLU attorneys. Leonard Weinglass, one of the attorneys defending the blacks, noted at last week's debate that a secret cache of weapons, including a .357 magnum revolver, clubs and knives, had been found where the Klansmen had been meeting. Referring to the Klan suit, Weinglass told Pancer, "This is not the typical political organization we are used to defending."

Aryeh Neier, national executive director of the ACLU, said in New York that he felt it was "proper" for the San Diego chapter to take the Klan case. Neier and other ACLU officials questioned officers on the Marine base last month.

Neier noted that Maj. Gen. Carl Hoffman, base commander at Pendleton, indicated he ordered the Klansmen transferred solely because of their membership in the Klan. Neier said this makes it an acceptable civil liberties issue.

"There has been some dissatisfaction over the prorities in taking this case," Neier admitted. "But whatever the priorities are, they must never be based on the political views of our clients."