South Carolina refused to let radioactive wastes from Three Mile Island be trucked to a dump inside its borders yesterday, and the Nuclear Regulatory Commission indicated that it will keep both reactors on the island shut down for a while, not just the one that went badly awry two weeks ago.

Heyward G. Shealy, of the South Carolina Department of Health and Environment Control, ordered two trucks carrying Three Mile Island wastes back toward Pennsylvania when one was in North Carolina and the other in Virginia. The wastes were en route from the site near Harrisburg to a burial site in Barnwell, S.C., when Shealy refused them entry.

"we take a lot of [nuclear] waste down here, but we don't want to take all of it for the whole country." Shealy said. "I don't think our citizens are interested in having to take all the dangerous stuff from Three Mile Island."

Even as Shealy ordered the waste trucks back toward Pennsylvania, officials at the NRC were telling reporters that the undamaged reactor at Three Mile Island will be shut down indefintely while they investigate the accident. The undamaged reactor, sister to the damaged one, is ready to begin generating electricity.

Harold C. Denton, director of NRC's Office of Reactor Regulations said he strongly opposes allowing Unit One to go back into operation. He said that in the investigation of what caused the March 28 accident at Unit Two, NRC inspectors and uncovered a violation of NRC rules on Unit One similar to rules violations it found on Unit Two.

"A valve on the steam line essential to Unit One was found in a closed position, which is one more example of a breakdown in procedures," Denton said in an interview. "I want to make sure the same type of accident we had here before doesn't happen again."

When the March 28 accident forced a shutdown of Three Mile Island's Unit Two, technicians at Metropolitan Edison Co. had just finished refueling the uranium core of Unit One, which supplies 819,000 kilowatts of electricity. Had the accident not happened to the 900,000-kilowatt Unit Two, the refueled reactor would probably already be generating electricity.

Keeping both Three Mile Island reactors shut down means Metropolitan Edison must go on paying an extra $1.1 million a day for outside electricity to supply its customers with power. It also raises the possibility of forced or rotating brownouts for Met Ed customers during peak summer air-conditioning periods if electricity is scarce in nearby regions.

"We don't know what this possibility means to our state," W. Wilson Goode, chairman of Pennsylvania's Public Utilities Commission, said in an interview. "We know that if Unit One is not going to come back on line, we've got problems."

Goode said the commission is about to have a formal proceeding to find out who should pay for the outside electricity Met Ed is buying to supply its customers.

"Consumer advocates have already asked us to freeze any fuel adjustment clauses to February's levels," Goode said. "I promise we will make a decision on this before the end of May."

The two trucks carrying waste to the Barnwell, S.C., burial ground were supposed to be carrying waste only from Unit One. But it was discovered yesterday that some of the waste in the trucks had come from Unit Two, where clothing and waste water was more badly contaminated by radioactivity.

"While the composition of the material was well within federal stands," Denton said, "we concluded that some of the water from Unit Two got in there."

Shealy said he won't allow the wastes to enter South Carolina until he has "written confirmation" about their contents. He said South Carolina already buries 80 percent of the nation's low-level waste. He said the NRC ought to consider shipping Three Mile Island's wastes to Hanford, Wash., which buries much of the nation's military wastes.

Denton said he wasn't sure why South Carolina refused entry to the Three Mile Island waste, but he said that if the matter isn't resolved soon it will create difficulties in disposing of the wastes from Unit Two. What's happening to the waste now? "It's sitting on the island," Denton said.

At the White House, President Carter announced the formation of the President's Commission on Three Mile Island to look into the causes of the accident. Carter named 11 persons to the commission, including:

John G. Kennedy, 52, president of Dartmouth University, named chairman; Bruce E. Babbitt, 40, governor of Arizona; Patrick E. Haggerty, 65, retired chairman of Texas Instruments Inc. and currently chairman of the board of trustees of Rockefeller University; Paul A. Marks, 52, vice president for health sciences at Columbia University and a physician; Harry C. McPherson Jr., 49, a Washington lawyer.

Also, Russell Peterson, 62, former governor of Delaware, former chairman of the President's Council on Environmental Quality and now president of the National Audubon Society; Cora B. Marrett, 36, associate professor of sociology at the University of Wisconsin; Lloyd McBride, 63, international president of the United Steelworkers of America; Thomas Pigford, 56, chairman of nuclear engineering at the University of California at Berkeley, and Theodore B. Taylor, professor at Princeton University and a onetime designer of atomic weapons.

The sole resident of Middletown, Pa., appointed was Ann Trunk, a 43-year-old mother of six who refused to evacuate her home 2 1/2 miles from the Three Miles Island site.

A high school graduate whose only contact with Three Mile Island was an open house visit in 1972, Trunk was baffled by her appointment.

Two-thirds of her neighbors left during the worst days of the accident, but the Trunks stayed put until last Sunday, when they left to avoid their returning neighbors.

"We were accused of being dumb. I had a couple of my friends accuse me of endangering my children," Trunk said in the living room of her modest home. "We left on Sunday to get away from the people coming back."