Religion is powerfully motivating and belligerent humans fight over it. Heck, religion has caused conflict even in my diverse and tolerant family. Taking our daughter to visit her Irish-Catholic relatives, I asked my husband to make sure they didn't give her any pork. Like Jews, Muslims steer clear of anything with an oink. My gentle, peaceable mate, wanting to avoid one of those conversations, said: "Mam, Yazzy doesn't like pork so don't give her any." A few days later, my beaming mother-in-law proudly announced: "She does like pork. I gave her some sausages and she ate them right up!" It took a few days for my blood pressure to return to normal.

Then again, humans also fight over small bits of compressed carbon, tracts of dirt, addictive mind-altering substances and soccer matches. It's not just religious ideology that causes problems – state-imposed atheism was a defining feature of brutal 20th century regimes led by Stalin, Tito, Mao Zedong, and Pol Pot among others, which resulted in the suffering and murder of millions. Tens of thousands of Russian Christians alone were executed for their beliefs by atheists intent on purging religion from the Soviet Union.

Yet it's true, religion has been a major feature in some historical conflicts and the most recent wave of modern terrorism. Religion has taken on extra significance today because globalisation is challenging and changing everything. Religious identity not only survives but can take on heightened significance when national and political alliances break apart, as happened in the former Yugoslavia in the early 1990s, when Serbs, Croats and Bosniacs were divided along Orthodox, Catholic and Muslim fault lines.

The Qur'an recognises the human propensity for conflict and gives permission for defensive warfare. Muslim scholars developed a just-war theory although admittedly in the ensuing centuries jihad was also used to further the territorial ambitions of ruthless leaders, just as today it's distorted to justify terrorist bombings. Like both law and politics, religion can be used to defend the oppressed and to oppress the defenceless.

The problem of corrupt religion has attracted the criticism of many prophets and saints. The Qur'an censures religious hypocrites:

Among the people there is he whose discourse on the life of the world pleases you, and he calls on God as witness to what is in his heart, yet he is an unyielding and antagonistic adversary. When he turns and leaves, he walks about corrupting the earth, destroying crops and livestock – God loves not corruption (Q2:204–205).

The verse could well apply to Saddam Hussein, who made a show of praying on television, but gassed and bombed Kurds and was a tyrannical dictator. Religion, unfortunately, provides a useful cover and powerful motivator for the evil-hearted. That religion can be so markedly different in the hands of the power-hungry, as opposed to the altruistic and virtuous, really says more about human psychology than it does about religion. That's why so many human conflicts unfortunately involve religion.

Alain de Botton, philosopher and author of Religion for Atheists, is worried about fundamentalism. "To say something along the lines of 'I'm an atheist: I think religions are not all bad' has become a dramatically peculiar thing to say," he told British journalist Bryan Appleyard in 2012. "If you do say it on the internet you will get savage messages calling you a fascist, an idiot or a fool. This is a very odd moment in our culture."

Neo-atheism, the belief that science is the only path to truth and all religions are equally deluded and destructive, has taken hold in much of the debate over atheism. The movement, whose keys figures include Richard Dawkins, the late Christopher Hitchens, Sam Harris and Daniel Dennett, is an ideology that arrogantly celebrates an understanding of everything through supposed reason and proof. It allows little doubt or questioning about the unknown. It also happens that some of these key figures, including Ayaan Hirsi Ali, are backers of state violence against Muslim countries since 11 September 2001.

It's clearly an exaggeration to suggest atheists are rampaging through the streets demanding the end of religious belief but the last decade has seen an ever-increasing number of atheists feeling the need to ridicule or damn people who do believe in a god.

Dawkins, at a dinner with de Botton and others in London in 2012, recounted a conversation he'd had with Hitchens. "Do you ever worry," Dawkins asked, "that if we win and, so to speak, destroy Christianity, that vacuum would be filled with Islam?"

It's a curious question that reflects both the vicious hatred of Muslims by many so-called new atheists but also a creepy utopian nightmare that is apparently idealised by them. Destroy Christianity? Because the Catholic Church has committed innumerable crimes, opposes abortion and birth control, refuses to accept female priests and hides sex offenders in its midst? To be sure, the institution is dysfunctional, but wishing for its disintegration reflects a savagery that will only inflame, not reduce tensions.

None of this is to excuse the undeniable barbarity unleashed by religionists over the centuries. The misogyny, beheadings, terrorism, killings, beatings and cruelty are real. They continue. Today we see a growing battle in the Middle East between Shi'ite and Sunni; a Jewish state unleashing militancy against Christian and Muslim Palestinians; and an anti-gay crusade led by some Jewish, Christian and Muslim leaders that threatens the sanctity of life itself.

I've been guilty of claiming religion is the source of the world's evils, but it's a careless comment. It's far too easy to blame the Muslim faith for honour killings. I'm under no illusion about the fact that religion is routinely used to justify the more heinous crimes. But the 20th century is filled with examples, namely Stalin's Soviet Union and Mao's China, that didn't need God as an excuse to commit genocide against a state's own people.

As 14 year-old Malala Yousafzai sat on a bus in the grounds of her school in Pakistan's Swat Valley, a gunman shot her in the head. After proudly claiming responsibility, the Taliban told the world that the teenage education activist's work represented "a new chapter of obscenity, and we have to finish this chapter". The "obscenity" was the education of girls.

The Taliban felt no shame. They know that what they have done is right because their god tells them so. Gods have been used to justify almost any cruelty, from burning heretics and stoning adulterers to crucifying Jesus himself.

On the other side of the world, Anders Behring Breivik slaughtered 77 Norwegians. Breivik seems to have seen his murderous spree as a way of getting rid of Muslims, yet his 1,500-page manifesto revealed, at best, a weak attachment to religious belief. To Breivik, Christianity seems important mainly because he sees it as white. Breivik, like the devoutly religious Taliban, also appears to feel no shame.

The men who flew planes into buildings on 9/11, the Pakistanis who went on a murderous rampage in Mumbai and the Bali bombers, all killed as many people as they could in the name of their religion. Breivik did it in the name of his race. Timothy McVeigh, who killed 168 people and wounded 800, hated the government. All saw their mass murder as a political act of protest and all felt justified.

Atheists like Mao or Pol Pot have murdered millions in the name of political totalitarianism. Hitler used a quasi-mystical racist philosophy to exploit the ancient hatred of the Jews by Christians. I heard somewhere (I've never been able to discover where) that terrorism occurs when you combine a sense of military and economic inferiority with a sense of moral superiority. Religion is very good at conferring a sense of moral superiority on its followers.

Indeed, while the religious have murdered throughout history in the name of their god, I've been unable to find any evidence of atheists killing anyone in the name of atheism. Atheists are no more or less capable of evil than anyone else, but it seems that murder, particularly mass murder and war, is a sin of commission. In other words, human beings are generally only prepared to fight and kill in the name of something. It can be a god, but it can also be a political philosophy – like nazism or communism. Many fight for patriotism: for country, tribe or race. Some kill because they're psychologically disturbed, but none – so far – in the name of atheism.

So, while I don't agree that only religion causes conflict, I'd argue that all mass murder and war are fought in the name of a bigger-than-self philosophy or idea. Atheism, simply lack of belief in a god, has not yet proved compelling enough to motivate murder. So far no one has gone into a crowded public space and blown themselves up while shouting, "No god is great!".

Religion has been implicated in all sorts of conflict and violence throughout human history. There is blood on the hands of the faithful, and no avoiding the fact that in the service of the wrong people, religion can be a force of great harm. This includes Christianity. If we consider the sins of the Christian past critics have plenty to work with – witch-hunts, the Crusades, Christian support of slavery.

But the picture is much more complex than is often implied. Take the Inquisition. Dinner party guests are likely to nod in agreement when someone mentions the "millions killed" at the hands of the church but historians now suggest around 5,000 – 6,000 over a 350-year period. That's less than 18 a year. One a year is terrible, but the reality appears a long way from what we are often served up.

Likewise the idea that most of the wars of history have been caused by religion is demonstrably false. The vast majority of wars have been conducted in the pursuit of profits or power, or waged for territory or tribal supremacy, even if religion has been caught up in those pursuits. But there is a very real sense in which religion can moderate those forces. David Hart notes that, "Religious conviction often provides the sole compelling reason for refusing to kill … or for seeking peace … the truth is that religion and irreligion are cultural variables, but killing is a human constant".

Of course millions were killed at the hands of Mao, Stalin and Pol Pot. To say their murderous totalitarianism had nothing to do with their atheism is to completely misunderstand them and the ideologies on which their actions rested. Yale theologian Miroslav Volf argues that as far as Christianity goes, it will only be violent if it is stripped of its content— thinned out - and infused with a different set of values. The story of Jesus gives absolutely no warrant for violence. Any believer behaving that way is disobeying the one they claim to be following.

The answer, Volf argues, to violence perpetrated in the name of the Cross, is not less Christianity but more – Christianity that is not depleted of its meaning but full of its original moral content, which is at its heart non-violent and a force for good.

When Martin Luther King Jr confronted racism in the white church in the South he called on those churches not to become more secular, but more Christian. King knew that the answer to racism and violence was not less Christianity but a deeper and truer Christianity. King gained his inspiration from the one who said that those who follow him must turn the other cheek, love their enemies and pray for those who persecuted them. His leadership of the civil rights struggle remains a fine example of love triumphing over hate; of costly and courageous resistance of evil and of religiously inspired social action that made the kind of difference that everyone can appreciate.