"Well, no one threw stones or bricks," said Professor Edward Shils of the University of Chicago, summing up the reaction to the Jefferson Lecture he had just given before about 1,000 people in the auditorium at the National Council for the Humanities.

The Jefferson Lecture assignment has plenty of prestige. But if you're speaking-as Shils did last night-about how the federal government interferes with the running of universities (including insistence on affirmative-action programs) often for poltical benefit, you might expect a rebuttal or two.

There were, in fact, a few raised eyebrows. But Shils, a small, cheerful man with gray hair, stood surrounded for the most part by friends and well-wishers at the reception afterward. "Usually people think I took so mean," he said. "They might have thought I'm a decrepit old man. But I think they were listening . It didn't sound too read, did it?"

A former student spoke up: "The interpolations were really delightful," said Simon Bourgin, who works at the State Department and studied with Shils in the '30s. (One interpolation: "We can't have everybody getting grants from the National Science Foundation and the like. Somebody's got to work and pay taxes")

"But . . . " Bourgin continued, "you read too quickly."

"But I had to cover it," Shils protested matter-of-factly.

"I know you had to cover it," Bourginsaid. "But you just went too fast. It was too much for me to get."

Shils continued talking enthusiastically, with the result that he never got near the huge spread of food and wine and soft drink. So someone brought him and entire silver platter of goodies.

Guests at the reception after the 45-minute lecture included people connected with the National Endowment for the Humanities, their state committee members, academics from near and far and others interested in the topic.

"Most of the people who've approached me are laudatory," said Shils. "One chap was a bit aggressive. I told someone if he had been a bit bigger I would have hit him. He was a fooliish fellow. He said, 'you're doing a disservice to the right cause.' Pfoo! I've heard all the arguments."

"You know, Professor Shils," said one man standing nearby, "yours was one of the best lectures in the past eight years of the series, because it was controversial. People didn't all agree with you."

"I thought it was a splendid beginning," said Alan Fern of the Library of Congress. "He addressed a very interesting problem. He feels the life of the university needs to be apart from the people who stand to profit from what comes out."

"I admire the force of Mr. Shils' intellect," said Joseph Duffey, head of the National Endowment for the Humanites who noted that it was the Council for the Humanities under his predecessor, Robald Berman, who was responsible for choosing Shils to be the Jefferson Lecturer this year. "I do not think," Duffey continued, "Professor Shils understands the social situation in this country."

When Duffey explained, before Shils began, why the Jefferson Elcutre was in praise of Jefferson, he noted that some of Jefferson's ideas may be "outdated" but that his intellectual spirit and drive were exemplary. "We are Jeffersonians in our questions, not in our answers," he said.

Howard University Law Professor Simeon McIntosh, one who disagreed with Shils' call for an intellectual meritocracy, countered later at the reception: "Doesn't Shils feel a university must have the responsibility to reach those he considers less academically qaualified-as part of the Jeffersonian democratic ideal?" CAPTION: Picture, Edward Shils, center, after last night's Jefferson Lecture; by James M. Thresher