Betty Dillon, coordinator of the United States Secretariat charged with all U.S. preparation for the United Nations-sponsored conference on women, to be held in Nairobi this summer, said yesterday that she resigned her $69,000-a-year post after six weeks on the job because of a disagreement over the secretariat's role.

"It was somewhat different than described to me last fall," Dillon said. "Then, it was anticipated that it would be larger and more directly involved but now it appears that it will have considerably less decision-making power. The way things have developed, the secretariat will have heavy input from other areas."

Part of that "heavy input" has already been felt. Maureen Reagan, named by her father to head the 37-member U.S. delegation, left no doubt at a dinner she gave for area delegates last week that she will have charge of preparations, including the briefing book, for the Nairobi conference.

Reagan also said she plans to have the entire American delegation come to Washington in May so everybody can get acquainted and, as one who was at the dinner put it, "speak with one voice."

"There's no question about not going to Nairobi," said the source of reports that the United States may pull out of Nairobi conference in the aftermath of the Soviets' determination to talk about "peace, disarmament and 'Star Wars' weaponry" at preliminary sessions in Vienna last month.

Dillon, who came out of semiretirement to head the secretariat and whose last assignment was in Montreal as U.S. minister to the International Civil Aviation Organization, said she had not been concerned by the "politicization" in Vienna. What did bother her, she said, was that "developing countries have so much at stake, something which isn't always appreciated by major countries whose women haven't had to sacrifice."

A source close to Dillon said that something else that bothered her was the role of the First Daughter.

Said one delegate of Reagan's stewardship: "It's going to be a very organized delegation."