On my way to Queen Street station last week, I passed a man standing in front of a board at which he was gesturing, like Captain Mainwaring explaining a tricky field manoeuvre.

"It all points," he said, looking at his complicated chart, "to the existence of a higher intelligence." A few yards on, a tangerine-robed Hare Krishna monk was collaring a couple, who had the stricken expression of those who knew they were now going to miss their train.

It was a fine example of the religious marketplace, believers of different hues vying for attention. Good luck to them, and to all Mormons, Jehovah's Witnesses, and evangelical Christians, as they tout their spiritual wares door to door. No-one can object to their proselytising, since we are free to ignore them. In some respects, though, religion still exerts an insidious hold on the way we all live. Thankfully, there are signs that this might soon be challenged.

Last week, a petition lodged at the Parliament by Secular Scotland asked the Government to change the rules on religious observance in schools. At the moment, all children must take part in Christian devotion unless their parents request otherwise. In the experience of the father who instigated the petition, that veto meant his daughter was left sitting alone while her chums sang hymns and chanted prayers. You don't need to be agnostic to see this isn't right.

A few days later, the Saltire Society published a pamphlet by Richard Holloway, former Bishop of Edinburgh, called A Plea For A Secular Scotland. A provocative call for a religion-free state, it is the first intellectual salvo in what one suspects will be a long, hard and necessary fight to free our society from institutionalised religious bias and indoctrination.

This is not to say religion should be banished or persecuted, but it is to ask that it be relegated to the purely private and personal realm. In so doing, the running of the country would be liberated from the sometimes – I would argue often – pernicious influence of religion, whether state-imposed Christianity, or that held by citizens of varying beliefs, be they Jewish, pagan, Muslim, or whatever.

As Holloway writes, antediluvian ideas found in sacred texts are viewed "not as the dated arrangements of a Bronze Age society but as eternal norms". In the name of Christianity Western society has thus perpetrated countless atrocities, among them slavery and the vicious oppression of women and gays. Other religions such as Islam and Judaism have been no more enlightened.

The desire for a secular state is not based on the belief that the non- religious are better people (their ethical record card is anything but unblemished), but on the principle that to run a country fairly and well it is necessary to remove supernatural, intractable and often primitive beliefs from the statute books. Religion by its very nature is built on intolerance and judgmentalism. It is exclusive and excluding. To observe the troubles in Turkey or Syria and across the Middle East, where Christians are in conflict with Muslims, Sunnis with Shias, Jews with Arabs, is to see how easily, and lethally religion divides and destroys.

Of course, a wholly secular state would require as much scrutiny as any governing body, but I like to think it would be more dispassionate and even-handed than one in thrall to the idea of an omnipotent, disembodied power. For instance, it would not allow churches to run their internal affairs outwith state law, as is the case at present, nor would it countenance faith schools or impose religious practice within the curriculum. It would, however, ensure pupils were taught about religion, and the part it has played in our history.

A secular Scotland would not tolerate sharia law or any other religious practices that do not conform to current legislation. And it would not be swayed by the lobbying of those whose religious convictions run in any way counter to a society based on equality for everyone. There's a very modern irony in all this that one can't avoid. A secular state is based on tolerance and respect for all. That means no matter how prejudiced or intolerant the beliefs of those under its care, it is duty-bound to protect them to the last letter of the law.