HERE we go again.

The Catholic Church is on the warpath. MSPs are in a tizzy. Family life is supposedly under attack. Brian Souter is stirring ominously. Could the Scottish Government split under the strain?

To many observers, the SNP’s consultation on gay marriage threatens a re-run of the poisonous Section 28 debate which blind-sided Donald Dewar’s administration in the first months of the Scottish Parliament. Back in 1999, it was a plan to repeal a Thatcher-era law banning councils from “promoting” homosexuality that got cardinals and tabloid editors in a lather, and prompted evangelical Stagecoach millionaire Brian Souter to bankroll a ballot under the banner of Keep The Clause. Without Section 28, we were told, classrooms would become laboratories of gay indoctrination. Society duly clasped its head in a Munch-like scream.

Now it’s the prospect of same-sex marriages that is making headlines and sending Alex Salmond into an emergency pow-wow with the Bishop of Paisley. The SNP’s iron discipline is slipping as socially conservative MSPs dissent. The party’s former leader Gordon Wilson wants a referendum on the issue to avert “social disintegration”. And Souter – now Sir Brian and the SNP’s biggest donor – is warning of a return to “Babylonian” values. As Prince almost sang, we’re going to rammy like it’s 1999. Right? Wrong.

In explaining why, it’s worth setting out the background. First, the law. At present, marriage in the UK can only take place between a man and woman. It can be either religious (church and/or religious celebrant) or civil (registrar). Civil partnerships, introduced for same-sex couples in 2005, are always secular. They can only be conducted by a registrar, and cannot – for now – happen in church. The debate is whether gay couples, currently restricted to civil partnerships, should also be able to marry, in a civil or religious ceremony.

It is this the SNP Government is consulting on. Ministers stress no faith would be forced to conduct a service against their beliefs. Indeed, only a few small players have shown interest in conducting gay marriages – Liberal Judaism, Unitarians, Quakers, the Metropolitan Community Church, and the Pagan Federation. Gay marriage is already legal in Argentina, Belgium, Canada, Iceland, Holland, Portugal, Spain, Norway, Sweden, South Africa and six US states.

Second, a little politics. There is no doubt the SNP has its dissenters. A recent parliamentary motion from Glasgow new boy John Mason, noting some people disagree with “same-sex sexual relationships”, was signed by three other SNP MSPs: David Thompson, Bill Walker and Dick Lyle. Thompson previously opposed the appointment of gay minister Scott Rennie to a kirk in Aberdeen as it was not “compatible to be a Christian and an active homosexual”. Walker later distinguished himself by saying he found the logo for a campaign against homophobia “intimidating” and Nazi-like. He was nominated by the gay-rights group Stonewall for a “Bigot of the Year” award. He finds out next month if he’s won.

But do these views really threaten the Government? “Look at any party membership and they’ve all got them, usually unreconstructed men,” sighs one former MSP. “But they don’t hold any more sway than a youth or a student wing.”

Even the Liberal Democrats have issues. Scots leader Willie Rennie slated the Catholic Church’s stance on gay marriage last week, but his office is supported by the evangelical charity CARE, which says redefining marriage to include same-sex couples is “deeply flawed and socially corrosive”. CARE’s Scottish spokesman is Gordon Macdonald, LibDem candidate in Eastwood earlier this year. The point is, all parties contain different opinions on gay marriage. The SNP doesn’t seem to have a disproportionate number of opponents. Indeed, its evangelical MSPs are offset by a clutch of gay MSPs elected in May.

Third, some history. Holyrood didn’t roll over on Section 28. MSPs voted to repeal it in 2000 regardless of the mauling from the Keep The Clause campaign, and the 86% vote for keeping it in Souter’s ballot. In England, it was repealed two years later. Despite the initial hysteria, classrooms did not start brainwashing. David Cameron later apologised for the Tories introducing Section 28, calling it “offensive to gay people”. There is no reason to suppose Holyrood would go to pieces now.

Nor is the reaction to the gay marriage proposal a surprise, in the way the fuss over Section 28 was. The same debate took place in the last Parliament, albeit at a low ebb. For two years Holyrood’s public petitions committee considered two petitions calling for same-sex marriages. Brought by the LGBT Network and Equal Marriage Campaign, they argued there should not be one law for heterosexual couples and another for homosexual couples – that was discrimination. In response, the Catholic Church argued gay marriage would break the “procreative nature” of marriage, and be a “profoundly unjust” innovation. The relevant minister said gay marriage was not a priority, and would only tangle with reserved laws such as tax and pensions. He also refused to set up an advisory committee on the subject.

The attitude led one SNP MSP to consider bringing a private member’s bill to force the issue. The minister was Fergus Ewing, one of two SNP MSPs not to vote for the repeal of Section 28 (the other was his mother, Winnie). The debate went nowhere because the SNP pulled down the shutters, but it learned what to expect.

So why the change? Why gay marriage now? Change at Westminster played a part. At the close of Gordon Brown’s premiership, a late amendment to the Equalities Bill paved the way for civil partnerships in religious premises south of the Border. It’s not gay marriage – the building can be religious but the service is still a civil partnership – but it’s a step in that direction. The pace quickened with the Coalition’s arrival. In February, Lynn Featherstone, LibDem Equalities Minister, said the Government would reform the “differences between civil marriage and civil partnerships”, with a consultation in May.

Against this backdrop Holyrood manifestos were made. The Scottish parties didn’t want to be left behind. The LibDems pledged to “extend legal marriage to gay couples”. The Greens to open “marriage and civil partnership up to mixed-sex and same-sex couples”.

More cautiously, Labour would “consult on options to provide genuine equality for same-sex couples”. The SNP would consult on “the questions of same-sex marriage and registration of civil partnership”. Only the Scottish Tories were mute.

But if the SNP manifesto line was a little half-hearted, its leader was not. During the election campaign, Alex Salmond told the Sunday Herald he supported gay marriage. “I’m very much against imposing it on any religion. But if a denomination is prepared to accept gay marriage then I’m in favour of it.”

The other big change was personality. In 2011, Nicola Sturgeon took over the equalities brief from Ewing and the line that gay marriage was neither a priority nor practical was abandoned. Some SNP MSPs encouraged gay-rights groups to lobby the party for progress. “It’s simply an idea whose time has come,” said one. Sturgeon, far more to the left than Ewing, also helped ensure a pledge appeared in the SNP manifesto.

On September 2, Sturgeon launched the Government consultation. Although heavily caveated, it opens up the possibility of same-sex marriage, both religious and civil. The rationale is clear. “The Government’s initial view is that marriage should be open to both same-sex couples and opposite-sex couples,” says the consultation document. “This view is grounded in our commitment to equality, and out of support for stable and committed relationships.”

The consultation runs to December 9, to be followed by draft legislation next year and a final bill in 2013. Sturgeon’s approach is in sharp contrast to Ewing’s. Instead of emphasising cross-Border problems, Sturgeon says Edinburgh will simply “discuss the practical implications with the UK Government”.

A fortnight after the Scottish consultation was launched, the UK Government announced it was delaying its own until March 2012, and would only consult on same-sex civil marriages by registrars. Same-sex religious marriages were ruled out, as were mixed-sex civil partnerships. This means the Scottish consultation offers a significant option – religious same-sex marriage – now closed off in England and Wales.

As in the petitions committee, the Catholic Church has come out against gay marriage as undermining an ancient institution. Cardinal Keith O’Brien says it would “demolish a universally recognised human right”. Philip Tartaglia, Bishop of Paisley, says ministers have no “authority to say what marriage is, or to change its nature to decree that people of the same sex can marry”. And Archbishop Mario Conti of Glasgow says they have no “mandate to reconstruct society on ideological grounds”.

Souter has also made a unique contribution to the debate by asking rhetorically: “Are we going to live in a Babylonian-Greek type of society, where sex is primarily a recreational activity, or are we going to stick with the Judeo-Christian tradition, where procreation is something that we want to put within a marriage context?”

Of these contributions, Tartaglia’s made the biggest impact, but only after the issue was piggybacked onto Salmond’s beleaguered anti-sectarianism bill. By suggesting the two issues were putting Catholics off the SNP, he secured an audience with the First Minister at Bute House. Then last week Gordon Wilson and David Robertson, an evangelical minister from Dundee, made their call for a referendum.

As Westminster dithers under pressure from the Catholic Church and Church of England, the SNP seem to be alone with their enemies on the field of battle as the sky darkens. But this is not a Section 28 moment. Holyrood has changed. MSPs have lost the rabbit-in-the-headlights look of 1999. The Parliament has a decade of legislation under its belt. Only last week the UK Supreme Court backed one of its biggest decisions (on asbestos compensation) and it will soon have a suite of new powers under the Scotland Bill. It won’t be easily cowed. And most parties are in favour. Scotland has also changed. In 2000, almost half the country, 48%, felt same-sex relationships were wrong. By 2010, it was 27%. Support for gay marriage rose from 41% to 61%.“Section 28 is very much ancient history,” says John Curtice, professor of politics at Strathclyde University. “Attitudes have changed dramatically. We’re living in a different world.”

Granted, the referendum idea is cute, as Salmond needs one for independence. But the rest is loopy, though no doubt sincere. Consider Wilson’s statement: oppressed by the “gay-rights lobby”, faiths are to be “compelled” to conduct same-sex marriages. State funds are being used to “demonise” those refusing to toe the elitist line. Christians are “bullied” by “secular zealots”. An “inevitable consequence” of gay marriage would be a “return to the values of a pagan society”. If it’s allowed, “logically” incest should be too.

It could be the creed of the survivalist. If Wilson’s name hadn’t been on the cover, it would have been roundly ignored. It is categorically not the spark for a schism in the SNP.

But Salmond is not out of the woods yet. He won’t get a re-run of Section 28, but there’s still the risk of a Bernie Ecclestone moment. When Labour watered down policy on TV tobacco advertising in 1997 after the Formula 1 boss donated £1m, Tony Blair famously wriggled out of it by insisting he (Blair) was a “pretty straight sort of guy”. But he never looked the same.

Remarkably for a leader in his fifth year in power, Salmond has yet to suffer a financial scandal. But if he dumped gay marriage, he could be embroiled in one. Told Souter’s views and that he gave the SNP £1.2m, some voters wouldn’t take long to join the dots – rightly or wrongly. So for the sake of perception, the First Minister could be obliged to snub Souter and press on. It could risk a lucrative relationship and antagonise the Church, but the alternative is looking like he’s in a donor’s pocket.

Gay marriage is coming, but religion and politics will never be a harmonious union.