The principal of a prominent Anglican school has broken ranks on LGBT discrimination, saying she wants no exemptions from legislation. .

The headmistress of Sceggs Darlinghurst in Sydney, Jenny Allum, said in a letter to parents she did not want the legal right to discriminate and “welcomes all – regardless of age, race, sexual orientation or religion”.

“There has been some media coverage about the bill in the Senate to remove exemptions from the Discrimination Act and the Fair Work Act,” Allum wrote.

“I want to make it clear that I don’t want Sceggs to have any exemption from any Discrimination Act or Fair Work Act based on our religion … I know we have students, staff, parents and alumni who are members of the LGBTIQ community. They are warmly welcome at Sceggs.”

On Wednesday 34 Sydney Anglican schools wrote to the federal education minister demanding he preserve a clause in the federal Sex Discrimination Act that allows religious schools to discriminate on the basis of sexuality, gender expression or marital status.

In addition to Allum, the principals of Cranbrook, Kambala, Sceggs Redlands and Shoalhaven Anglican School were among those who did not sign the letter.

The government has indicated it may remove the exemption. On Wednesday more than 1,000 students and former students of the 34 schools wrote to their principals asking them to remove the “right to discriminate”.

One principal who signed the letter, the headmaster of St Andrew’s school, told Guardian Australia on Friday it had been misinterpreted and the exemption was something “we don’t actually want”.

John Collier said the issue had been misreported by media, and his school would never expel a student or sack a teacher for being gay.

He said he wanted the exemption removed, but that it should be retained as a “temporary expediency” until it could be replaced with other protections for religious freedom.

Collier said he agreed with Allum’s stance.

“We agree with our critics,” he said. “It’s ironic. Heads of schools are actually advancing the same argument as the critics.

“What we Anglican heads are saying is these exemptions are uncomfortable, that they operate in the area of discrimination, and let’s get rid of them. But only get rid of them when can replace them with positive terms which protect our rights to suit our ethos.”

He said religious schools needed the right to hire teachers who agreed with the school’s beliefs in the same way that environmental organisations only hired people who believed in climate change.

He said the exemption in the Sex Discrimination Act was unwanted but was “the only legal protection that schools currently have”.

“It’s the only thing we can cling to, and it’s very partial and we don’t actually want it,” he said. “It doesn’t really [protect the ethos of the school]. But there is not very rich legislation in the field. Schools rely on anything.

“We agree we don’t actually want the exemptions but they have got to stay there. Many of our old students have said now ‘we understand, and that’s fine’… People are reacting against trigger words which they have misconstructed,” he said.

He said St Andrews had not contributed to the drafting of the letter, but that it had been written by a group of other Anglican heads of school.

The letter sent to the minister describes the exemption in the Sex Discrimination Act as “clumsy”.

“The current exemptions … are really the only significant legal protections available to schools to maintain their ethos and values in regard to core issues of faith. A more general positive right would be far better, but until such time … the exemptions should remain.”

On Friday, the head of Barker College – another signatory – wrote on the school’s website that he was “dismayed” by the reaction to the letter.

“It is clear the letter has been perceived as a message of discrimination and cruelty. Such a message was never intended and I am truly distressed to see this impact.”

In her letter, Allum maintained that Sceggs had good relations with the Sydney diocese, despite disagreeing with the letter.

“Sceggs is operated by a company, Sceggs Darlinghurst Limited,” she wrote. “We are, however, proudly an Anglican school, and we have always had excellent relationships with the diocese of Sydney. I expect that to continue.

“The Anglican church is, and has always been, a broad church, and there is a great diversity of views within it. I expect that we will be able to negotiate any issues with the same sensitivity and strength we have shown when controversial issues have been raised in the past.”

