In Tariq Ali's autobiography, Street Fighting Years, the veteran radical recalls his culture shock at arriving as a student at Oxford in 1963. His prior education had been under the military dictatorship of Pakistan, where he would not dare to share atheistic thoughts, even in whispers to his closest friends.

"When I first saw a pimpled youth, wearing a tattered crimson corduroy jacket standing on a chair in front of a stand at the freshers' fair and shouting at the top of his voice, 'Down With God,' I was both excited and moved. In fact I was a trifle incredulous, which must have explained the fact that I just stood there and stared. Finally, a bit embarrassed, the man in the corduroy jacket stepped down and recruited me to the Oxford University humanist group. I was to discover, much to my surprise, that debates here were much more stimulating than those conducted within the careerist confines of the Labour club."

Fifty years later, almost to the day, student atheist groups have been recruiting once again. At the LSE – an institution that in Ali's day was notorious for anti-establishment, free-thinking radicalism – Abishek Phadnis and Chris Moos from the atheist society were threatened with ejection from their own freshers' fair by student union staff and security. Their offence was wearing T-shirts featuring cartoons from the hugely popular online comic series Jesus and Mo. They were told that wearing the shirts was creating an "offensive environment" and were asked to cover them up. The students then received a hand-delivered letter from the LSE secretary, asking them to refrain from wearing the T-shirts and warning that the school "reserves the right to consider taking further action if warranted".

Meanwhile in Reading, this year the atheist, humanist and secularist society has been expelled from the student union altogether. The decision follows a similar row at the 2012 freshers' fair, when the society decorated their stall with a pineapple, to which they had attached a post-it note bearing the name Mohammed. As the group explained at the time, in services to both historical accuracy and comedy: "After a few minutes, we were told by another member of RUSU staff that 'either the pineapple goes, or you do', whereupon they seized the pineapple and tried to leave. However, the pineapple was swiftly returned, and shortly was displayed again, with the name Mohammed changed to that of Jesus."

A student union, like any institution, is duty bound to protect all its members from hatred, discrimination, intimidation or threats of violence. In neither of these instances is this relevant. Jesus and Mo is anti-religious satire at its best, invariably humane, intelligent and often very funny. The cartoons are miles removed from the grotesque, demeaning caricatures of some of the notorious Jyllands-Posten cartoons of 2005. Meanwhile, calling a pineapple Mohammed (or, for that matter, Jesus) has the approximate intellectual depth of saying "knickers" to the vicar. However when such a gesture is made in solidarity with untold hundreds of people currently imprisoned or facing corporal or even capital punishment for crimes of blasphemy around the world, it is surely considerably more offensive to restrict and punish such expression than it is to utter it in the first place.

Freshers' fairs at all universities present the first taste of a new life for hundreds of thousands of young people every year. Most leave the confines of the family home and the intellectual limitations of schools. Thousands more arrive from overseas, including many from countries where freedom of religious expression is severely curtailed. Some students arrive with sincere and devout religious conviction, and no one should question their right to retain and exercise their beliefs. But how many others arrive, like the young Tariq Ali, relishing hitherto unimagined freedom of thought and belief? How many would be similarly inspired in their thinking, their political and personal development, to know that British universities are places where religious beliefs can not only be freely exercised, but freely challenged, even mocked?

Grumbling old farts like me often bemoan the diminishing radicalism of students. Often it is unfair – we place expectations on young people from which the rest of us seem exempt. But 50 years after Ali had his moment of revelation, a mere five years after we finally got around to abolishing the blasphemy law in England and Wales, I find it sad and disturbing that students themselves, and the administrators of their institutions, appear to be voluntarily forbidding anti-religious expression.

We face challenges in 2013 that did not exist 50 years ago. Religious hatred, particularly Islamophobia, is a real and corrosive influence in political and media discourse and it needs to be challenged and resisted. However when such efforts extend to echoing and mirroring the most heavy-handed restraints on freedom of thought and expression, effectively imposing a theocratic, fundamentalist rulebook on believers and non-believers alike, it is a victory not for progressive liberalism but for dogmatic oppression.

• This article was amended on 11 October 2013. We originally stated that Phadnis and Moos were ejected from the freshers' fair. In fact, they were threatened with expulsion unless the t-shirts were covered. This has now been corrected