After Salman Rushdie published The Satanic Verses, religious "scholars" doubted whether the Ayatollah Khomeini had the right to order his murder. They had no liberal qualms about executing a writer for subjecting religion to imaginative scrutiny. They believed that blasphemers and apostates must die as their religion insisted. But only if they were citizens of an Islamic state. As Rushdie was living in London in 1989, a free man in a free country, the clerics concluded that religious law did not apply to him.

The Rushdie controversy was the Dreyfus affair of the late 20th century. It established today's dividing lines between the secular and the authoritarian, between those who were willing to defend freedom of thought and inquiry and those who wanted to censor and self-censor to keep fanatics happy. We can gauge how low we have sunk by remembering that at the start of the battle 23 years ago there was a tiny regard for the forms of legality, even among those who were otherwise happy to condemn free thinkers to death. However brutal they were, they respected their version of due process.

The Islamist murders first of Salmaan Taseer and then of Shahbaz Bhatti show that what tiny scruples blood-soaked men possessed vanished long ago. The best way to describe the terror which is reducing Pakistani liberals to silence is to enumerate what the assassins did not allege. They did not say that Taseer and Bhatti must die because they were apostates – or, to put that "crime" in plain language, because they were adults who decided they no longer believed in the Muslim god. Taseer had not renounced Islam. Bhatti could not renounce it as he was the bravest Christian in Pakistan, who campaigned for equal rights for persecuted minorities with the dignity and physical courage of a modern Martin Luther King.

Nor did their assassins claim that their targets had committed the capital crime of blasphemy. Taseer and Bhatti had not said that the Koran, like the Talmud and the New Testament, was the work of men not god. They did not denounce Muhammad's morality or offer any criticism of his life and teaching. If you wanted to reduce the whirling, brilliant narrative of Rushdie's Satanic Verses to a single sentence, you could say that it was in part a "blasphemous" account of the early history of Islam. Taseer and Bhatti attempted nothing so brave. They confined themselves to making the modest point that Pakistan's death penalty for blasphemy was excessive and barbaric, and that was enough to condemn them. Their killers murdered them for the previously unknown crime of advocating law reform: blew them away for the new offence of blaspheming against blasphemy.

One Pakistani journalist I spoke to described his fellow liberals as members of a persecuted minority, who now knew that if they spoke out, they would be shot down. Salmaan Taseer's daughter, Shehrbano, wrote a heartbreaking piece for the Guardian in which she despaired of a "spineless" Pakistani elite that was too frightened to praise her father or condemn his murderers.

In the networked world, censorship by the authoritarian state or clerical paramilitaries is meant to matter less. Technology enthusiasts can point to Twitter revolutions as proof of how emancipatory democratic ideas seep into apparently closed societies. But the ideas that Pakistanis need from America, Europe or "the west" to help fight armed theocracy are not there for surfers to find.

Fear plays its part in keeping western opinion quiet as well. It is hard to credit, but liberal society responded pretty well to the threat to Rushdie in 1989. Penguin refused to withdraw the Satanic Verses. Booksellers ignored threats and bombs and carried on selling it. But once the global wave of terror had passed, no one wanted to put themselves through what Rushdie and Penguin had been through, and a silence descended. Even the supposedly militant "new atheists," whom genteel commentators damn for their vulgarity, steer clear of religions that might kill them. Close readers of Richard Dawkins will notice that almost all his examples of clerical folly are drawn from the Catholic and American evangelical churches, whose congregations are unlikely to firebomb his publishers.

The fear is still present. Last month, four men were convicted of slashing the face and fracturing the skull of Gary Smith, a London teacher who had made the mistake of taking the windy official pronouncements about "promoting diversity" seriously and taught Muslim girls about Christianity, Judaism and Hinduism. Political violence comes from the British National Party, English Defence League and various splinter groups from the IRA, as well as Islamists, and that is before you raise your gaze and examine the assorted gun-totting crazies who inhabit the fringe of American politics.

The difference between Islamism and the rest is that liberals are happy to denounce white extremists, while covering up militant Islam with the wet blanket of political correctness. They do not confine themselves to saying that, of course, society must protect people from being murdered for their religion, as Slobodan Milosevic murdered the Bosnian Muslims, and punish employers who refuse jobs to members of creeds they dislike, as Protestant employers in Northern Ireland once refused to hire Catholics. They maintain it is illicit to criticise religious ideas. Thus, along with the admittedly faint fear of violence, western writers who want to provide arguments against religious misogyny, homophobia, racism and censorship must also live with the fear that their contemporaries will accuse them of orientalism or Islamophobia.

The world may pay a price for the monumental blunder of treating religious ideologies – which are beliefs that men and women ought to be free to accept or reject – as if they were ethnicities, which no man or woman can change. Not the smallest reason why the Arab revolution is such an optimistic event is that al-Qaida and the Muslim Brotherhood have been left as gawping bystanders. Their isolation cannot last. Eventually, if Arab states move towards democracy, there will be a confrontation with political Islam. Arab liberals, like Pakistani liberals, will search the net for guidance. They will discover that far from offering strategies that might help, timorous western liberals have convinced themselves that it is "racist" to criticise raging fanatics who no longer even bother to pretend that they are anything other than liberalism's mortal enemies.