Rosie Waterhouse: Will the voice of moderate Muslims be heard at City?

I wrote an opinion piece in this space three months ago, headlined "Universities must take action on Muslim extremism". Naively, I did not anticipate the furore that followed. I was moved to write because of my anxieties about the increasingly confrontational activities of the student Islamic Society at City University London where I teach. They had staged events with the "brothers" and "sisters" segregated, invited radical Islamist speakers and planned to show a DVD of the Yemen-based preacher Anwar al-Awlaki, who has been banned from Britain for his alleged links to terrorists. The DVD was not shown after the then vice-chancellor, Malcolm Gillies, intervened.

In February, more than 100 Muslim men staged Friday prayers on the pavement outside the university's main entrance. At the same time, a dozen female students wearing the the niqab – a veil covering their face apart from their eyes – handed out leaflets saying the protest was because the Islamic Society had been given a multi-faith space as their prayer room. "It is impermissible for Muslims to offer prayers in a place where other than our Lord, Allah, is worshipped", it said.

I called on universities to be more vigilant in monitoring the literature being handed out and the links on the Islamic Society website to supporters of extremist ideology.

I also said that the niqab should be banned in universities. One of my journalism students, a Muslim woman, had interviewed a group of female students who said they started wearing it only after coming to City and joining the Islamic Society. In Taliban strongholds in Afghanistan, females are forced to cover up and are denied an education. To me, the wearing of the niqab was a sign these students had been radicalised at university.

This unleashed a torrent of hostile comment on The Independent website, which ran to 17 pages. I was accused of being a racist and Islamaphobic. Several posts said I should resign or be sacked. Copies of the article were posted around the journalism department at City, with invitations to add comments. Most were angry and critical.

A colleague, Paul Anderson, wrote an article on his blog saying universities were secular institutions and supporting my stance against the potential promotion of violent extremism on campus (although he was not in favour of a niqab ban).

In May, while on holiday overseas, I received a text message from Anderson saying my photograph and his had been posted on the Islamic Society website together with a diatribe accusing us of being Islamaphobic and harbouring "outright hatred" of all Muslims. To me, this was a deeply disturbing and palpable threat. I contacted Anderson and the acting vice-chancellor, Professor Julius Weinberg, to instruct the Islamic Society to remove my photograph and the offending article.

Anderson telephoned the Islamic Society president Saleh Patel. He explained how upset I was at this perceived threat, and wanted the items removed, but Patel refused. When I returned to university, I felt all eyes were on me. To my distress, the Islamic Society continued to refuse to remove my photograph or the article. They might not have contained any overt personal threat but they were intimidating, at the very least.

It took almost two weeks and the intervention of the vice-chancellor, the students' union and, eventually, the police before my photograph and Anderson's were removed. The article stayed. Relations deteriorated and the Islamic Society was deregistered as a recognised society of the students' union. Their website has been taken down.

So, where do we go from here? The acting vice-chancellor maintains that a multi-faith prayer room is permissible according to numerous Muslim scholars – many Muslims use it. He will only allow an Islamic society to be reconstituted as a more inclusive Muslim faith organisation that agrees to adhere to the university's core values and principles – which exclude gender segregation and advocating violence.

City University is not alone in learning how to deal with potential Islamic extremism. Several prominent members of student Islamic societies have been convicted of terrorism. Universities UK has established a working group to investigate the scale of the problem and work out how to proceed.

Most students have left for the summer break. Come September, it remains to be seen whether a newly constituted Islamic faith group – one which allows the voice of moderate Muslims to be heard – will have a recruitment stall at Freshers' Week.

The writer is director of the MA in investigative journalism at City University London