United Nations Ambassador Jeane Kirkpatrick has withdrawn as commencement speaker at Trinity College here in the wake of spirited controversy on the Roman Catholic campus over her position on El Salvador.

Kirkpatrick, a Trinity faculty member from 1962 to 1967, had been invited as commencement speaker in October of last year. He acceptance was announced on campus last February, a time when Catholic protests over the Reagan administration's El Salvador policy ran high.

The ambassador telephoned to withdraw on April 16 "because of the developing controversy on campus, to which she did not want to be a party," said a spokesman for Trinity's president, Sister Rose Ann Fleming.

Fleming, who was reported to be involved in end-of-the-year board meetings, could not be reached yesterday for comment, but Vicki Sidoti, college press officer, said, "Sister Rose Ann wants to make it clear that she [Kirkpatrick] was not disinvited" by the college.

At the United Nations, an aide to Kirkpatrick said "she's not going to make any comment" on the matter and referred inquiries to Fleming.

Between February and April 16, the controversy over the choice of Kirkpatrick as commencement speaker surged in the campus newspaper, in student meetings, in prayer vigils and in an outpouring of letters both to Kirkpatrick and to the college administration.

Carol Connelly, a graduating senior who opposed the invitation, said that although there was by no means agreement on campus on the issue, "most [of the graduating seniors] would have been willing to wear a red arm band" as a sign of protest, had Kirkpatrick been the speaker.

In addition, she said, a number of faculty would not have come to the commencement exercise, scheduled for May 17. "It seems that the graduation is going to be a lot smoother" with Kirkpatrick out of the picture, Connelly said.

American Catholic bishops and members of religious orders have spearheaded opposition to Reagan administration policy of increasing military aid to the government of El Salvador. They were particularly infuriated by a comment of Kirkpatrick's that four American Catholic missionaries murdered here last December were "not just nuns [but] political activists."

Sister Helen James John, head of Trinity's philosophy department, who recalled sharing ideas with Kirkpatrick at the women's school in the '60s, wrote her former colleague in early April that "you have become internationally prominent as both a shaper and an eloquent advocate of a position directly opposed to a global concern for social justice and human rights."

Meanwhile, across town, Georgetown University yesterday confirmed that Kirkpatrick remains "a possibility" for commencement speaker at the Jesuit university, where she taught political science before taking a leave to serve the Reagan administration.