John Haldane, a professor of philosophy at St Andrews University and a leading commentator on Scottish Catholic affairs, said the Cardinal Keith O'Brien scandal was a challenge for the church to reform. The process, he added, should include cutting the number of dioceses north of the Border by 50%.
Mr Haldane also suggested a committee of about six lay advisers be formed to see it through the transformation.
Currently five of the eight dioceses are without bishops, numerous parishes are struggling to find priests and finances are also dire in many areas.
The three priests and a former priest who made allegations of inappropriate behaviour against O'Brien said they felt vindicated after he admitted sexual misconduct.
Catherine Deveney, the journalist who broke the story last week, said she had spoken to the four men, who were "relieved at being vindicated" adding none of the accusers was pursuing a personal vendetta against O'Brien. She added: "There is obvious sadness for Keith O'Brien as a man, but this wasn't about just Keith O'Brien the man but about Keith O'Brien the cardinal. So there is a mixture of sadness, a bit of relief they have been vindicated and I would say there has also been a little bit of anger it took all of this to get to where we are.
"One of the individuals concerned said that to take the cardinal on as an individual himself would have been like running into a brick wall.
"These men are spiritual men. They want to see an open and transparent Catholic Church as a result of this, they don't want to see it destroyed."
Colin MacFarlane, of Stonewall Scotland, part of the gay rights group which gave Cardinal O'Brien a Bigot of the Year award last year for his anti-gay marriage stance, hopes to discuss the language used in the debate over same-sex marriage with the church's leadership soon.
Mr MacFarlane accepted the Catholic Church had teachings on the issue but said he took issue with the "grotesque" language used primarily by Cardinal O'Brien, whose downfall he said was "a personal tragedy".
Gay rights campaigner Peter Tatchell said an estimated 40% of Catholic priests are gay. He added: "Studies documented by Father Donald Cozzens in the US suggest 23% to 58% of the clergy have a homosexual orientation, with the figure being closer to 60% among younger priests.
"Recent revelations in Italy have alleged the existence of gay cardinals and other Vatican officials, and their involvement in gay bars, clubs, saunas, online chat rooms and male prostitution services. Given their denunciation of homosexuality, how can they live with their conscience?"
Businessman Sir Tom Farmer, who denied he was sheltering the fallen church leader from the media, said he had taken the deliberate decision of not finding out where Cardinal O'Brien had gone to escape the fallout from his dramatic fall from grace.
Asked if he knew the whereabouts of the former leader of the Catholic Church in Britain, the Kwik-Fit tycoon said: "It's not the case he's staying in any property belonging to me. I don't know even now. I purposefully said to everyone I didn't want to know where he is nor will I try to find out where he is."