The claim was made after a Presbyterian minister resigned after being investigated for attending the 2024 Pride parade in Dublin.
Reverend Dr Katherine Meyer was ruled by a church court to have failed to "yield submission in the Lord to the courts of the Church".
A Presbyterian Church spokesperson said the resignation of anyone from the Church was "a matter of regret".'
One of the most painful decisions of my life'
In a statement to BBC News NI, Rev Dr Meyer said resigning from her ministry was "one of the most painful decisions of my life".
"Like any intelligent woman of my generation, I have worked a lifetime in historically patriarchal institutions," she said.
Rev Dr Meyer also said that she had faced complaints because of "my pastoral support for members of the LGBTQ+ community and my appearance in public in their company".
Speaking about her resignation, a spokesperson for the Presbyterian Church in Ireland said that the resignation of anyone from the Church was "a matter of regret", but added that it was "ultimately a personal decision for each individual".
"However, we recognise that this resignation was offered within the context of judicial processes within the Church," the spokesperson continued.
"During the course of a recent hearing regarding a further complaint concerning Dr Meyer, the Commission dealing with the matter was informed by her that she intended to resign as an ordained minister of the Church.
"This was stated before the Commission had completed its consultation, let alone come to any conclusions.
"Having been informed of Dr Meyer's intention to resign, the Commission chose not to issue any formal sanction."
But she also faced the further church investigation into complaints that she attended the Dublin Pride parade in 2024.
That investigation led to a hearing by a Presbyterian Church in Ireland Judicial Commission—a church court—held in Belfast on 29 November.
"The Judicial Commission concludes that the primary issue is Dr Meyer's ongoing failure to "yield submission in the Lord to the courts of the Church", verging on defiance of the very courts to which in her ordination vows she has promised to yield submission," their subsequent judgement said.
Following that hearing on 29 November, Rev Dr Meyer decided to resign from her ministry at a meeting of Dublin and Munster Presbytery.
Some Presbyterian ministers from that Presbytery had made some of the complaints against her.
As a result of her resignation, Rev Dr Meyer can no longer do things like officiate at weddings or conduct services of baptism or communion
When contacted by BBC News NI, Rev Dr Meyer gave a statement in response confirming she had resigned.
"It has become impossible for me to cooperate any further with the enquiry and disciplinary processes to which I have been subjected and which, in my experience, have been so flawed and destructive," she said.
"Over recent years, a series of complaints have been lodged against me, resulting in a number of disciplinary actions.
"The particular claim which has been the common theme of these acts of discipline, as best as I can determine, is that by my teaching and actions I have disrupted the peace and unity of the Church.
"And further, that following censure, I failed to seek to preserve that peace and unity."
Rev Dr Meyer said that "precisely how [she] did this was never clearly stated but assumed".
She said the trigger for the complaints seemed to have been her "pastoral support for members of the LGBTQ+ community and [her] appearance in public in their company, although this was never specifically stated".
Resigning was the 'only path'
Rev Dr Meyer said that she had "co-operated fully, thoughtfully, and clearly" with each investigation.
"However, in the wake of the most recent complaint, I could have no further illusions about where the latest enquiry was heading," she continued.
"To my great sorrow, therefore, I decided that the only path forward for me was to resign from ordained ministry.
"It was not a decision I welcomed, but on this occasion I could only follow my conscience."
Professor Whelan had also attended the Dublin Pride Parade in 2024.
Professor Whelan told BBC News NI that Rev Dr Meyer had told the church court of "the rights of conscience in matters of ethical decision making, and the tradition of loyal dissent within the Reformed and specifically Presbyterian church tradition."
"There seems to be a new sin in the Presbyterian Church in Ireland: the sin of public truth-telling," Professor Whelan continued.
