The war within the Liberal party over freedom of religion will be a defining issue of the Coalition’s third term.

If people of faith thought freedom of religion was settled with the re-election of Scott Morrison to the Prime Ministership they should think again.

Last night’s ABC QandA program revealed that the issue is far from settled within the Liberal Party itself.

There is going to be a messy fight by rainbow-left members of the Liberals such as last night’s panellist Tim Wilson. Christians and Christian schools are by no means in the clear.

One of Morrison’s most influential backbenchers holds very different views about freedom than the Christian and conservative voters who flocked back to the Liberals in the “miracle” election.

Wilson, a former Australian Human Rights Commissioner and now member for Goldstein in Victoria, made it very clear that in his view religion has enjoyed privileges which must now be wound back.

This of course is contrary to all of the public campaigning of the Yes campaign during the postal plebiscite which said there would be “no consequences” for anyone else’s freedoms and that the No campaign’s assertions to the contrary were “red herrings” and “furphies”.

Fast-forward to last night and questioner Ruth McKie is raising concerns about freedom of religion and parents’ rights (scroll down to first question). The latter is a reference to compulsory radical gay sex and gender fluid education in schools, something John Howard has repeatedly raised.

She also mentioned in her question the unprecedented prayer and fasting of Christians in the lead up to the election

In response, Wilson revealed his views on what he obviously believes is a privileged status that Christianity has enjoyed.

He made it clear that there was a time when freedom of religion “transcended” the rights of other Australians, particularly LGBTI Australians.

Here’s what he said: “Anti-discrimination legislation, which is frankly the basis of these concerns, was debated at a time when freedom of religion transcended the rights of other minority groups within the community, particularly LGBTI Australians, and I think we need to look at that law and improve it so that everybody’s rights are protected rather than just tinker with existing law.”

Now this task of “improving” anti-discrimination law so “everybody’s rights are protected” has been given to the Australian Law Reform Commission.

But in my view, this is mission impossible. When there are two competing truth claims about the definition of marriage (and gender), it is impossible to protect everybody’s rights.

Wilson was quite wrong to say that anti-discrimination law has not previously considered LGBTIQ issues.

Anti-discrimination legislation at state and federal level has long prohibited discrimination on the basis of sexuality or gender identity.

It has balanced competing rights to freedom by making religious organisations such as churches, mosques and schools exempt.

This has allowed them to employ staff who share the religious community’s ethos and to continue to be free to teach their views on morality and human flourishing.

The exemptions meant that LGBTQ activists were not free to impose their world view on religious organisations and it meant discrimination against LGBTIQ people in the wider society was unlawful.

It is the same freedom enjoyed by political parties who are free to positively discriminate in favour of staff who believe what the party believes.

It would be ludicrous if the greens were unable to turn away a coal mining executive from applying for a job with the party.

In a technical sense perhaps Wilson was right in that this exemption means the rights of religion do transcend the rights of LGBTI people within those religious communities.

But that is just common sense unless the real agenda is to de-authorise a religious community’s views on sexuality, gender and marriage.

Surely pluralism and tolerance means making space for competing views? That of course is what the exemption sought to do.

But I don’t think this is what Tim Wilson means.

Exemptions are by no means perfect and it would have been better if freedom of religion was expressed as a positive freedom able to override anti-discrimination law.

That might be where some in the Liberal party hope the ALRC will land but the rainbow left, emboldened by the change to the definition of marriage, will not wear this.

Wilson, who was one of the five rebel Liberal MPs who wanted the Coalition to break its promise to hold a peoples’ vote on marriage and legislate with Labor and the Greens, clearly thinks religion must give way to the new LGBTIQ agenda.

Interestingly, Wilson did not take up the part of Ruth McKie’s question referring to parents’ rights to have their children kept free from radical LGBTIQ sex and gender fluid indoctrination at school.

Labor’s Attorney General Mark Dreyfus was also quite disingenuous last night on the issue of Christian schools and their concerns about Labor’s plan to strip them of the freedom to employ staff who share the parents’ values on marriage and gender.

He conflated the faux issue of schools expelling kids because they are same-sex attracted.

Sure, the Ruddock review into religious freedom identified that in a technical sense the exemptions under anti-discrimination law allow this, but it is a power not sought or used by Christian schools.

Everyone is happy to drop this provision but that is not what the concern at the election was about.

Yet this is used with great emotional force to beat up on Christians and Christian schools as being “anti-gay”.

Dreyfus did not even address the substance of the concern raised with him last night which was freedom in employment decisions for schools.

Host Tony Jones seemed so blinded by his rainbow-green-left view of the world that all nuance and therefore opportunity for intelligent follow-up questions were lost.

Labor and the Greens remain deeply hostile to religious freedom. They are clear that the change to marriage law means the rainbow political movement has won and Christians and others are bigoted and must yield.

Thankfully they are not in government.

However, a significant group within the Liberal party agree with them.

The trouble is those within the Liberal party who support freedom and tolerance have been too timid to have the debate in public and the public are confused.

If the Christian and conservative voters who were so spooked by Labor’s anti-freedom agenda and came running back to the Coalition are not to be disappointed, Liberal MPs and Senators are going to have to speak up. Soon.

The Liberals’ rainbow-left led by Wilson have already begun staking out their ground.

It’s time those within the Liberals who believe in freedom did the same.

For Christians and freedom-loving conservatives, this will be the defining issue of the Coalition’s third term.