Enten Eller, a pacifist who said God directed him not to sign a draft registration card, was ordered today to perform two years of alternative service as punishment for his refusal to register for the standby military draft.

U.S. District Judge James C. Turk denied a request by federal prosecutors that Eller, the first registration resister convicted after the standby draft was implemented by President Carter in 1980, receive a two-year prison term.

The decision marked the latest development in a Reagan administration campaign to encourage registration among about 675,000 young men it says have failed to comply with Selective Service laws. The American Civil Liberties Union and other groups have attacked the standby draft as both illegal and unnecessary.

Turk, who clearly had little desire to imprison Eller, told reporters after today's 12-minute hearing that he found the polite, 21-year-old Bridgewater College senior "an especially unique individual . . . . He's in a funny position. He can't register for the draft. He can't bring himself to do it."

Eller told the judge as much today, apologizing for his failure to comply with the terms of an earlier sentence that directed he register. "I'm sorry I did not comply with the conditions of probation . . . but I felt I had no other choice," Eller said softly. "I hope we can work it out in a way that's acceptable not only to the government and myself but to your conscience."

The maximum penalty for failure to register is five years in prison and a $10,000 fine. Under provisions of the Youth Corrections Act, the law that Turk invoked in initially sentencing Eller last August, he could have received up to six years' incarceration.

Eller, a member of the pacifist Church of the Brethren and an honors student at the church-affiliated college near Harrisonburg, Va., has said God directed him not to sign up for the draft, a belief Turk said he found sincere.

Outside the federal courthouse here, a smiling Eller said he had been prepared to go to prison. "I had to be," he said. Asked if the judge's decision was a victory against the government, Eller replied: "I wouldn't put it in terms of a victory. If you want to put it in those terms, there's a victory whenever you follow your conscience."

Turk, who called Eller's actions "a substantial violation" of probation conditions imposed after his Aug. 17 conviction, said the young man's alternative service will be performed without pay at a Veterans Administration hospital in the Roanoke area or a similar facility.

Eller will be allowed first to complete college, the judge said. He is expected to graduate in May.

Turk had placed Eller on three years' probation, on condition he register for the draft within 90 days. Eller said after his one-day August trial he had no intention of complying with the order and he was true to his word.

The Justice Department has obtained indictments against 13 men it says have failed to sign the cards. Five have been convicted. Of those, two have received prison terms of up to 30 months, but are free pending appeal. A third was sentenced to two years' alternative service in a mental hospital. The fourth is awaiting sentencing.

A federal judge in California last month dismissed one indictment on grounds Carter's order implementing draft registration was technically flawed. Turk told reporters Eller refused to allow two local lawyers hired by his church to seek a delay in today's hearing to await the outcome of a government appeal of the judge's decision.

The sole witness in today's hearing was Eller's probation officer, Jimmy Lee, who said Eller had complied with every condition of his probation, including performing community service in Harrisonburg, except to sign the draft card.

Afterward, about 50 of Eller's church supporters moved forward in the courtroom to shake Eller's hand and several thanked Turk for being "so gracious." Eller slipped out a side door to find a telephone, he said later, to pass the news to his parents in California.