This is a column condemning cowardice – including my own. It begins with the story of a novel you cannot read. The Jewel of Medina was written by a journalist called Sherry Jones. It recounts the life of Aisha, a girl who was married off at the age of six to a 50-year-old man called Mohamed ibn Abdallah. On her wedding day, Aisha was playing on a see-saw outside her home. Inside, she was being betrothed. The first she knew of it was when she was banned from playing out in the street with the other children. When she was nine, she was taken to live with her husband, now 53. He had sex with her. When she was 14, she was accused of adultery with a man closer to her own age. Not long after, Mohamed decreed that his wives must cover their faces and bodies, even though no other women in Arabia did.

You cannot read this story today – except in the Koran and the Hadith. The man Mohamed ibn Abdallah became known to Muslims as "the Prophet Mohamed", so our ability to explore this story is stunted. The Jewel of Medina was bought by Random House and primed to be a best-seller – before a University of Texas teacher saw proofs and declared it "a national security issue". Random House had visions of a re-run of the Rushdie or the Danish cartoons affairs. Sherry Jones's publisher has pulped the book. It's gone.

In Europe, we are finally abolishing the lingering blasphemy laws that hinder criticism of Christianity. But they are being succeeded by a new blasphemy law preventing criticism of Islam – enforced not by the state, but by jihadis. I seriously considered not writing this column, but the right to criticise religion is as precious – and hard-won – as the right to criticise government. We have to use it or lose it.

Some people will instantly ask: why bother criticising religion if it causes so much hassle? The answer is: look back at our history. How did Christianity lose its ability to terrorise people with phantasms of sin and Hell? How did it stop spreading shame about natural urges – pre-marital sex, masturbation or homosexuality? Because critics pored over the religion's stories and found gaping holes of logic or morality in them. They asked questions. How could an angel inseminate a virgin? Why does the Old Testament God command his followers to commit genocide? How can a man survive inside a whale?

Reinterpretation and ridicule crow-barred Christianity open. Ask enough tough questions and faith is inevitably pushed farther and farther back into the misty realm of metaphor – where it is less likely to inspire people to kill and die for it. But doubtful Muslims, and the atheists who support them, are being prevented from following this path. They cannot ask: what does it reveal about Mohamed that he married a young girl, or that he massacred a village of Jews who refused to follow him? You don't have to murder many Theo Van Goghs or pulp many Sherry Joneses to intimidate the rest. The greatest censorship is internal: it is in all the books that will never be written and all the films that will never be shot, because we are afraid.

We need to acknowledge the double-standard – and that it will cost Muslims in the end. Insulating a religion from criticism – surrounding it with an electric fence called "respect" – keeps it stunted at its most infantile and fundamentalist stage. The smart, questioning and instinctively moral Muslims – the majority – learn to be silent, or are shunned (at best). What would Christianity be like today if George Eliot, Mark Twain and Bertrand Russell had all been pulped? Take the most revolting rural Alabama church, and metastasise it.

Since Jones has brought it up, let us look at Mohamed's marriage to Aisha as a model for how we can conduct this conversation. It is true those were different times, and it may have been normal for grown men to have sex with prepubescent girls. The sources are not clear on this point. But whatever culture you live in, having sex when your body is not physically developed can be an excruciatingly painful experience. Among Vikings, it was more normal than today to have your arm chopped off, but that didn't mean it wasn't agony. If anything, Jones's book whitewashes this, suggesting that Mohamed's "gentleness" meant Aisha enjoyed it.

The story of Aisha also prompts another fundamentalist-busting discussion. You cannot say that Mohamed's decision to marry a young girl has to be judged by the standards of his time, and then demand that we follow his moral standards to the letter. Either we should follow his example literally, or we should critically evaluate it and choose for ourselves. Discussing this contradiction inevitably injects doubt – the mortal enemy of fanaticism (on The Independent's Open House blog later today, I'll be discussing how Aisha has become the central issue in a debate in Yemen about children and forced marriage).

So why do many people who cheer The Life Of Brian and Jerry Springer: The Opera turn into clucking Mary Whitehouses when it comes to Islam? If a book about Christ was being dumped because fanatics in Mississippi might object, we would be enraged. I feel this too. I am ashamed to say I would be more scathing if I was discussing Christianity. One reason is fear: the image of Theo Van Gogh lying on a pavement crying "Can't we just talk about this?" Of course we rationalise it, by asking: does one joke, one column, one novel make much difference? No. But cumulatively? Absolutely.

The other reason is more honourable, if flawed. There is very real and rising prejudice against Muslims across the West. The BBC recently sent out identically-qualified CVs to hundreds of employers. Those with Muslim names were 50 per cent less likely to get interviews. Criticisms of Islamic texts are sometimes used to justify US or Israeli military atrocities. Some critics of Muslims – Geert Wilders or Martin Amis – moot mass human rights abuses here in Europe. So some secularists reason: I have plenty of criticisms of Judaism, but I wouldn't choose to articulate them in Germany in 1933. Why try to question Islam now, when Muslims are being attacked by bigots?

But I live in the Muslim majority East End of London, and this isn't Weimar Germany. Muslims are secure enough to deal with some tough questions. It is condescending to treat Muslims like excitable children who cannot cope with the probing, mocking treatment we hand out to Christianity, Judaism and Buddhism. It is perfectly consistent to protect Muslims from bigotry while challenging the bigotries and absurdities within their holy texts.

There is now a pincer movement trying to silence critical discussion of Islam. To one side, fanatics threaten to kill you; to the other, critics call you "Islamophobic". But consistent atheism is not racism. On the contrary: it treats all people as mature adults who can cope with rational questions. When we pulp books out of fear of fundamentalism, we are decapitating the most precious freedom we have.

j.hari@independent.co.uk