Australians concerned about freedom of religion in this country would be well advised to look beyond the present and likely future debate over same-sex marriage.

Already, what was until recently the traditional view, that marriage is a union between a man and a woman, is being presented as offensive at best and discriminatory at worst by some who advocate what they term marriage equality.

It is not only many believers who hold the traditional view about marriage. However, it is possible that the Catholic Church and some other Christian denominations, plus adherents of Hinduism and Islam, will be targeted for their attitudes on this issue by government tribunals and the like in the future. The first instance is already manifesting itself in Tasmania with respect to the Catholic Church.

For an example of how current government-funded institutions regard religion, attention should be given to the Royal Commission into Institutional Responses to Child Sexual Abuse. The royal commission has done good work in revealing the extent of mainly historical cases of child sexual abuse in churches and secular and government institutions up until relatively recent times.

Evidence before the royal commission indicates that sexual abuse was at a high level in the Catholic Church until about two decades ago, particularly in Victoria in the archdiocese of Melbourne and the diocese of Ballarat in the 1970s, 80s and early 90s.

The Catholic Church has never been a democracy. Each archdiocese or diocese is ruled by an archbishop or bishop respectively who reports directly to the Pope in Rome.

Evidence given to the royal commission and the Victorian parliamentary inquiry demonstrates that Frank Little (archbishop of Melbourne from 1974 to 1996) and Ronald Mulkearns (bishop of Ballarat from 1971 to 1997) knew of instances of pedophilia in their areas of responsibility but covered them up.

George Pell was the first archbishop or bishop to act against child sexual abuse when he set up the Melbourne Response in 1996, just three months after being appointed archbishop of Melbourne. This was the first time Pell had been in charge of an archdiocese or diocese.

Even so, Pell has very much been the target of the royal commission. It could be that such an expensive and longstanding organisation wants a high-profile target. And Pell is one of the best known Australians. Moreover, the cardinal has an international reputation and is the third most senior figure in the Vatican.

Pell already has appeared before the royal commission twice, once in person and once by video link from Rome. He also appeared in person at the Victorian parliamentary inquiry.

It has been known for some time that Pell has a heart condition. Yet on December 11 royal commission chairman Peter McClellan dismissed the cardinal’s request to give evidence via video link from Rome. This despite the fact Pell had a doctor’s certificate stating he was unfit to undertake long-distance air travel and that other witnesses, resident in Australia, had given evidence by video link.

Clearly the royal commission wants Pell in the witness box, even though such a personal appearance is most unlikely to change his evidence.

In the hearings last month, many of the high-profile claims about what Pell allegedly was told concerning child sex abuse between two and four decades ago collapsed under cross-examination from the cardinal’s lawyers.

It may be that the royal commission has a secondary agenda — namely, by focusing on the conservative Pell, it hopes to influence the Catholic Church to move to a less theologically conservative mindset.

Two case studies illustrate the point.

On August 24 last year, the royal commission interviewed Geoffrey Robinson. The retired bishop is a progressive and a critic of Pell. Despite anticipation in the media, he said little about Pell except that he and many of his colleagues disliked the cardinal. But Robinson declared that, in the late 1980s, he regarded Mulkearns as “one of the more forward-looking bishops”.

Towards the end of his testimony, Robinson criticised “obligatory celibacy” for priests and what he termed the “creeping infallibility” of the Pope. Much to the apparent satisfaction of counsel assisting, Gail Furness SC.

Last month, John Walshe, the parish priest of Mentone in Melbourne, was called to the witness stand for several hours across two days. This followed his decision to make a statement supporting Pell’s recall of a phone conversation with child sex abuse victim David Ridsdale.

Counsel assisting, Angus Stewart SC, accused Walshe of having “fabricated” evidence because of his friendship with Pell. It was never suggested that any witnesses critical of Pell might be guilty of fabricating evidence because of their enmity towards the cardinal.

Before this exchange, Stewart put it to Walshe that he had “similar viewpoints on theological questions” to that of Pell, including “a conservative theology of priesthood and sexual morality”. McClellan later intervened to imply that there should be a “greater role” for “women in the church”. Later still, McClellan did not intervene when counsel for one of the victims raised issues such as married priests and even the Latin mass. None of this is directly related to clerical child sexual abuse.

The church in Victoria is divided into the archdiocese of Melbourne plus the dioceses of Ballarat, Sale and Sandhurst (based at Bendigo). The members of the hierarchy who most frequently turned a blind eye to the crimes of their priests were Little and Mulkearns in Melbourne and Ballarat respectively. Neither was a theological conservative. On the available evidence there was much less child sexual abuse in Sale and Sandhurst, where there was a conservative tradition.

It has been reported subsequently on the ABC and in Fairfax Media that, when a young priest, Walshe was found by church authorities to have had an improper sexual relationship with an 18-year-old seminarian. This was a serious indiscretion but not a crime. However, neither news organisation has covered the recent revelation in The Australian that one of Pell’s most high-profile accusers is a convicted pedophile.

The lack of balance in the media’s reporting of child sexual abuse in the Catholic Church reflects the fact many journalists detest Pell’s conservatism. There are disturbing signs that a similar disposition is evident in the royal commission, which runs the risk of breaching the division between church and state.