Asserting that strategic arms limitation talks with the Soviet Union must continue to be isolated from all other aspects of Soviet-American relations because failure poses the danger of "mutual annihilation," Secretary of State Cyrus R. Vance strongly defended yesterday his decision to fly to Geneva today for a new round of negotiations.

At a news conference, Vance acknowledged that the Russian decision to place two well-known dissidents on trial two days before his meeting with Soviet Foreign Minister Andrei A. Gromyko in Geneva "has aggravated" Soviet-American relations.

This theme was echoed by White House press secretary Jody Powell, who deplored the trials in more fore-full terms in a separate meeting with reporters. Powell called the Soviet action "a sign of weakness on the part of those very forces of oppression and injustice which we protest," and he vowed that President Carter would continue his human rights campaign.

Both Vance and Powell alluded to a possible reexamination of other aspects of Soviet-American relations because of the trials of Anatoly Scharansky and Alexander Ginaburg. But they declined to list possible retaliatory steps that might be under consideration, and they specifically exempted the strategic arms talks from being affected by the general downturn in relations.

The talks "affect the peace of the world," Vance told reporters. "This issue must be treated differently from others and should be addressed on a continuing basis with the highest priority."

The administration's reaffirmation of the duality involved in continuing both the human rights campaign and the strategic arms limitation talks (SALT) negotiations followed sharp attacks on the White House's handling of both matters by Sen. Henry M. Jackson (D-Wash.) and Sen. Bob Dole (R-Kan.), who called on Vance to cancel the Geneva trip.This suggestion was also reportedly made by lower-level U.S. officials over the weekend but was not seriously considered by the president, according to a senior administration source.

Jackson said in a television interview that the Vance trip was 'the wrong signal at the wrong time." Dole introduced a resolution in the Senate calling on Carter to suspend all bilateral scientific and cultural exchanges with Moscow and to suspend indefinitely the SALT negotiations.

Vance's 10-day trip will include a two-day stop in London for talks between the foreign ministers of Egypt and Israel. In Bonn he will join the president for a state visit and the economic summit meeting of leading industrial nations.

But American Soviet relations dominated the press conference, accounting for half of 26 questions asked by reporters. Vance repeatedly stressed both the administration's condemnation of Russian attitude on human rights and the determination not to let the strains impede SALT negotiations.

"The trials violate fundamental principles of justice . . . It will inevitably affect the climate of relations and impose obstacles to the building of confidence and cooperation between our two countries," Vance said. But in response to a question, the secretary said he believed a SALT treaty would be agreed upon and ultimately ratified by the Senate despite the new strains.

Vance also said no decision has been reached on deploying the mobile MX missile, an item that he is expected to discuss with Gromyko. He indicated that the United States will want to keep this option open, a step that could win vital support for a treaty from conservatives.

On another topic Vance reported progress in American efforts to arrange a peaceful transition to independence for the disputed territory of Namibia (South West Africa) now ruled South Africa. He said that representative of the United States, Britain, France, West Germany and Canada are now in Angola negotiating with SWAPO, an African guerrilla organization.

"There only remain two questions to be resolved" before an agreement can be taken to the United Nations, said, but he did not elaborate.