All those responsible for the moral education of Enten Eller can take pride. They have done well. Eller is the 20-year-old college senior who the other day became one of the nation's first men to be indicted for not registering for the draft.

As the U.S. attorney for the western district of Virginia moves in to corner his quarry--if convicted, the Bridgewater (Va.) College physics major faces five years in prison and a $10,000 fine --Eller is drawing on the strengths of what he learned from his family, church and teachers. He is telling the state that, for moral reasons, some laws aren't worth obeying.

"I am a nonregistrant in order to be faithful to God, my conscience and my church," says Eller, a member of the pacifist Church of the Brethren. "Christ's way, the way of love, the way of concern for all peoples, the way of nonviolent peace, cannot be reconciled with the military, which uses killing and destruction, or the threat of such, to achieve its end."

If it were only moderately crafty, the Reagan administration would have ignored someone as thoughtful and devout as Eller and instead sent the posse for a 20-year-old unbathed drug- taking long-haired ex-juvenile delinquent who hangs out at the video game arcade. Those charms must have been possessed by at least a few of the 570,000 draft-age men who haven't registered in the past two years.

But Eller is a son any American parent could take pride in. He has a straight A average in school. He has short hair, reads his Bible and is so polite to his elders that he regularly called the U.S. attorney to stay current on the dates of his indictment and arraignment.

In seeking to imprison Eller, the Justice Department's strategy is to alert the other half-million resisters that everybody is vulnerable, starting with the clean-cut. This use of fear is an odd way of recruiting an army. With no persuasive case being made either that we are under unusual enemy threat or that we would be undermanned if we were, the draft registration campaign is really an issue of government thought control.

Enten Eller is indicted because the state seeks to dictate to a young man's conscience when it has no arguments to appeal to his intellect. It can't persuade him by reason, so it will control him by prison.

But what kind of soldier would an Eller make if suddenly he changed his mind and said to the bosses of the Selective Service that, because he is afraid of jail, he agrees to go into the army?

If the administration understood history, the way it doesn't understand pacifism and conscience, the Justice Department would see that it is unwittingly helping the peace movement by singling out Eller. The government is challenging a tradition that includes jailed pacifists from George Fox, who wrote the enduring "Quaker peace testimony" in Derby Gaol 300 years ago, to J. F. Powers, the American novelist who did 13 months in a federal prison rather than cooperate with the military during World War II. All Eller is saying these days on his way to court is a rephrasing of what Fox, Powers and numberless others of strong will and informed conscience said in their day. Their words have lasted.

The names of some 160 other young men have been sent to the Justice Department for prosecution. According to draft counseling groups, most of these are "self-reporters." They have, like Eller, told the government of their conscientious objections. They aren't hiding or bounding off to Canada and Sweden.

The waste of the government's time and money in this useless roundup could have been avoided had the registration cards contained a box for conscientious objection. Sen. Mark Hatfield (R-Ore.) offered that option when the legislation was in Congress. But the administration opposed it, and the proposal was defeated.

Young men of courage like Eller are now seen by the administration as taunters. That's as backward as the larger reality. There is no draft, no recruit shortage, no war and no space in prison. And now the government wants no dissent.