THE kitchen of his East Renfrewshire home suggests the joyful chaos of life with five young children.

On the kitchen table is a display of home baking that would put Mary Berry to shame; a shiny new coffee maker is making all the right noises as it froths up the milk for our cappuccinos.

Peter Kearney isn't exactly wearing a pinny, but as he fusses about in his jeans and slippers with a J-cloth in his hand, you imagine it's a look that would suit him very well. Actually, the cupcakes were made by his 17-year-old daughter Louisa, for whom baking is an antidote to the stress of sitting Highers. And the coffee machine was a 50th birthday gift.

Kearney, who was widowed in 2008, is both father and mother to his daugher and four younger sons. His wife Andrea died at 41, a year after being diagnosed with cancer while 38 weeks pregnant with their youngest, Philip, who recently made his First Communion – an important rite of passage for young Catholics.

Kearney says living with the loss gets harder as the years go on. "The rawness does dull, but that's all; it just dulls," he says. "It can flare up at any moment. I know Andrea misses being with us through all the milestone moments, and that is hard to bear."

He formed a charity in Andrea's name to help fund research into cancer in pregnancy, and is busy with arrangements for the annual fundraising dinner on Saturday.

Later on the day we meet, the Vatican confirms it has sent Kearney's disgraced former boss, Cardinal Keith O'Brien, into exile for a period of penance and prayer following cataclysmic revelations of homosexual activity. The move signals the Holy See's direct involvement in an unprecedented series of events that ended in Cardinal O'Brien, pictured below, stepping down as president of the Catholic Bishops' Conference of Scotland – thus renouncing his position as Scotland's most senior Catholic cleric – and declining to attend the papal conclave in March, even though he would have been Britain's only representative. The crisis was described by one Scottish Catholic academic as "probably the gravest single public crisis to hit the Catholic Church in Scotland since the Reformation".

Allegations of Cardinal O'Brien's inappropriate behaviour, made directly to the Vatican by three priests and one former priest, had been prompted by the announcement of Pope Benedict XVI's shock resignation two weeks earlier on February 11 – the day after Kearney's 50th birthday. They were made directly to Rome because otherwise Cardinal O'Brien, voted Bigot of the Year 2012 by gay charity Stonewall for his stance against same-sex marriage, would have been facing his own accusers and there were fears of a cover-up.

Since the cardinal was his line manager, it was down to Kearney to answer media calls throughout the night of Saturday February 23 after a Sunday newspaper posted its exclusive online at 9.30pm. He received the first inquiry at 9.40pm, and by midnight was fielding calls from media organisations in New York, Washington and Tokyo.

"I'd never handled anything like that before. The sheer scale of it was bigger than anything I'd ever dealt with, including the Pope's visit to Scotland in 2010," Kearney recalls. "I'd already made arrangements for broadcast journalists to interview Cardinal O'Brien in Rome after the conclave, so it was easy for them to switch swiftly to this new development. I got 100 calls that Saturday night alone. They all wanted to know: 'Is it true about the allegations of inappropriate sexual behaviour? Is he going to the conclave?'"

The bombshell had been brewing behind the scenes and Kearney says he knew nothing about it until that weekend. "It was really, really difficult to find myself in the position of asking those sorts of questions to someone I'd worked with very closely over the years. But I was in it, and could not run away."

Although the cardinal has now left the country, Kearney still speaks on behalf of the bishops' conference and his new line manager is its new president, Archbishop of Glasgow Philip Tartaglia. Given Cardinal O'Brien's absence, plus the fact there are five vacancies for the post of bishop in Scotland's eight dioceses, the collective voice of the Catholic Church in Scotland is considerably weaker then it was in, say, Cardinal Winning's time.

All of which, observers say, has catapulted Kearney into the position of being the most powerful lay Catholic, if not lay Christian, in Scotland. He says: "My voice is heard, my advice is taken, and there is respect given [from colleagues within the church]."

Much of the pressure of the job is offset by running on his treadmill at home. "In any crisis you're bound to have a higher profile and the last few months have certainly been frantic, but in terms of stress it doesn't even come close to the experience of personal loss," he says. "Honestly, this is not stress. After Andrea died I remember telling the children: 'Look at it this way. As you grow older you'll encounter challenges like exams, your driving test, and so on. But you'll be able to cope with them because you know what true stress is. This will make you stronger.'"

An honours graduate in politics from Glasgow University, Kearney – whose father was an NHS physiotherapist in Stirling and whose mother is a former primary school and special needs teacher from Barra –began his professional life as a commercial underwriter for General Accident Insurance in Perth. He says the experience of working in a commercial environment taught him the benefits of being organised and structured.

He stood for the deputy leadership of the SNP in 2000 but left the party when he joined the church in 2001. He is at odds with the SNP over its plans to introduce same-sex marriage in 2015, but remains committed to Scottish independence.

"You can't agree with everything, and it's the party I have most in common with. I still personally support independence for Scotland."

He acknowledges his job is political. "The Scottish Government is not sovereign like Westminster and doesn't have its hands on full power. While the big- ticket issues are out of its reach, politicians are left to focus on low-level social issues and have moved into the fields of morality and ethics that haven't been legislated before.

"There's a narrow, stifling social and moral consensus in Scottish politics at the moment, where every party supports things like same-sex marriage. That makes it quite difficult to have a national debate.

"The church is there to give the other perspective. That has grown its profile and given it the confidence to speak out. The same-sex lifestyle can be harmful to the health of those involved, as evidenced in the recent Stonewall report."

He believes the church should establish a counselling service for men, including clergy, experiencing same-sex attraction. He acknowledges people can be born gay, and stresses that the church has never been against gay orientation – and he holds to its teaching that gay people "should not indulge".

He also maintains that hostilility towards Catholics remains, and reveals he received 1000 "bold and obscene" emails from followers of the atheist Richard Dawkins after he posted on his blog that Kearney was "a nasty little weasel" for urging the SFA to sack head of referee development Hugh Dallas because he forwarded an offensive email cartoon of Pope Benedict prior to his visit to Scotland.

Kearney says: "Scotland remains a hostile environment for Catholics to live in. Priests have bricks thrown through their bedroom windows. The number of crimes motivated by anti-Catholic intolerance has gone up every year since the 2003 Criminal Justice Act was created. Things are not getting better."

Would a Yes vote change things? "We have to be grown-up and mature enough to take the decisions other countries have to make all the time. That won't happen without a sovereign Scottish Government with full powers – and the end of the Act of Settlement. If in the US a black man couldn't become president or head of state you couldn't possibly say there was no discrimination against black people."

How would independence affect the church in Scotland when it is at its weakest? "The church is already independent. It sees Scotland, England, Wales and Northern Ireland as separate entities. It's all the more important we get more bishops – and there's nothing I've seen to say that the appointment process is not under way.

"So the transition we would need to make to align with a sovereign Scottish Government wouldn't be that great."

Andrea, he says, was always very soothing and supportive and I wonder who is his spiritual adviser now that she is gone. He answers that he has many priests who are firm family friends and that he values his enduring connection to Barra, where he spent his childhood holidays and where his mother Anne returned to live following his father's death in 2002.

"When I'm there I feel part of an unbroken pre-Reformation Catholic tradition, which is reassuring and a great source of strength for me," he says.

And now, with the children off to school, he must rush back to the office – and another day of phone calls.