The Bible has thousands of passages that may serve as the basis for instruction and inspiration. Not all of them are appropriate in all circumstances.

The story of Saul and the Amalekites is a case in point. It's not a pretty story, and it is often used by people who don't intend to do pretty things. In the book of 1 Samuel (15:3), God said to Saul:

"Now go, attack the Amalekites, and totally destroy all that belongs to them. Do not spare them; put to death men and women, children and infants, cattle and sheep, camels and donkeys."

Saul dutifully exterminated the women, the children, the babies and all of the men – but then he spared the king. He also saved some of the tastier looking calves and lambs. God was furious with him for his failure to finish the job.

The story of the Amalekites has been used to justify genocide throughout the ages. According to Pennsylvania State University Professor Philip Jenkins, a contributing editor for the American Conservative, the Puritans used this passage when they wanted to get rid of the Native American tribes. Catholics used it against Protestants, Protestants against Catholics. "In Rwanda in 1994, Hutu preachers invoked King Saul's memory to justify the total slaughter of their Tutsi neighbors," writes Jenkins in his 2011 book, Laying Down the Sword: Why We Can't Ignore the Bible's Violent Verses (HarperCollins).

This fall, more than 100,000 American public school children, ranging in age from four to 12, are scheduled to receive instruction in the lessons of Saul and the Amalekites in the comfort of their own public school classrooms. The instruction, which features in the second week of a weekly "Bible study" course, will come from the Good News Club, an after-school program sponsored by a group called the Child Evangelism Fellowship (CEF). The aim of the CEF is to convert young children to a fundamentalist form of the Christian faith and recruit their peers to the club.

There are now over 3,200 clubs in public elementary schools, up more than sevenfold since the 2001 supreme court decision, Good News Club v Milford Central School, effectively required schools to include such clubs in their after-school programing.

The CEF has been teaching the story of the Amalekites at least since 1973. In its earlier curriculum materials, CEF was euphemistic about the bloodshed, saying simply that "the Amalekites were completely defeated." In the most recent version of the curriculum, however, the group is quite eager to drive the message home to its elementary school students. The first thing the curriculum makes clear is that if God gives instructions to kill a group of people, you must kill every last one:

"You are to go and completely destroy the Amalekites (AM-uh-leck-ites) – people, animals, every living thing. Nothing shall be left."

"That was pretty clear, wasn't it?" the manual tells the teachers to say to the kids.

Even more important, the Good News Club wants the children to know, the Amalakites were targeted for destruction on account of their religion, or lack of it. The instruction manual reads:

"The Amalekites had heard about Israel's true and living God many years before, but they refused to believe in him. The Amalekites refused to believe in God and God had promised punishment."

The instruction manual goes on to champion obedience in all things. In fact, pretty much every lesson that the Good News Club gives involves reminding children that they must, at all costs, obey. If God tells you to kill nonbelievers, he really wants you to kill them all. No questions asked, no exceptions allowed.

Asking if Saul would "pass the test" of obedience, the text points to Saul's failure to annihilate every last Amalekite, posing the rhetorical question:

"If you are asked to do something, how much of it do you need to do before you can say, 'I did it!'?"

"If only Saul had been willing to seek God for strength to obey!" the lesson concludes.

A review question in the textbook seeks to drive the point home further:

"How did King Saul only partly obey God when he attacked the Amalekites? (He did not completely destroy as God had commanded, he kept the king and some of the animals alive.)"

The CEF and the legal advocacy groups that have been responsible for its tremendous success over the past ten years are determined to "Knock down all doors, all the barriers, to all 65,000 public elementary schools in America and take the Gospel to this open mission field now! Not later, now!" in the words of a keynote speaker at the CEF's national convention in 2010. The CEF wants to operate in the public schools, rather than in churches, because they know that young children associate the public schools with authority and are unable to distinguish between activities that take place in a school and those that are sponsored by the school.

In the majority opinion that opened the door to Good News Clubs, supreme court Justice Clarence Thomas reasoned that the activities of the CEF were not really religious, after all. He said that they could be characterized, for legal purposes, "as the teaching of morals and character development from a particular viewpoint".

As Justices Souter and Stevens pointed out in their dissents, however, the claim is preposterous: the CEF plainly aims to teach religious doctrines and conduct services of worship. Thomas's claim is particularly ironic in view of the fact that the CEF makes quite clear its intent to teach that no amount of moral or ethical behavior (pdf) can spare a nonbeliever from an eternity in hell.

Good News Clubs should not be in America's public elementary schools. As I explain in my book, The Good News Club: The Christian Right's Stealth Assault on America's Children, the club exists mainly to give small children the false impression that their public school supports a particular creed. The clubs' presence has produced a paradoxical entanglement of church and state that has ripped apart communities, degraded public education, and undermined religious freedom.

The CEF's new emphasis on the genocide of nonbelievers makes a bad situation worse. Exterminist rhetoric has been on the rise among some segments of the far right, including some religious groups. At what point do we start taking talk of genocide seriously? How would we feel about a nonreligious group that instructs its students that if they should ever receive an order to commit genocide, they should fulfill it to the letter?

And finally, when does a religious group qualify as a "hate group"?

• On 11 June, the online edition of Guardian Letters published the following response from the Child Evangelism Fellowship:

The story of Saul and the Amalekites (1 Samuel 15:3) is found in any version or edition of the Bibles of the Jewish, Catholic and Protestant faiths since the first manuscripts were inscribed. Only a misinterpretation of the cited passage could be used to buttress genocide (How Christian fundamentalists plan to teach genocide to schoolchildren, 30 May). The goal of Child Evangelism Fellowship is the proper teaching of this passage, which is not an instruction in genocide. Though truly many brutal acts appear in both the Old and New Testaments, including the torture and crucifixion of Jesus by the Romans, nothing could be more un-Christian than the promotion of genocide of any group of human beings under the New Covenant introduced to the world by Jesus Christ. CEF and the Good News Clubs would never teach children that God would instruct them, or anyone today, to commit genocide. Reese R Kauffman

President, Child Evangelism Fellowship

Katherine Stewart replies: