It might have been hoped that Archbishop Philip Tartaglia, who runs the archdiocese until a successor is chosen, might have seen the need for a fresh start. But the signs are not encouraging.
One of the most harmful decisions his disgraced predecessor took was to cave in to a pushy and forceful colleague and agree to the breaking up and dispersal of a unified set of church archives.
A millennium of religious documents and artefacts had been painstakingly assembled and a permanent home found for them at Columba House in Edinburgh’s New Town during the second half of the last century.
This had been one of the priorities of Gordon Gray, Scotland’s cardinal from 1969 to 1993.
He wanted the Church to shed its image as a phenomenon bound up with the immigrant enclave. A key plank of this strategy was to demonstrate what the church had contributed to the making of Scotland both before and after the Reformation.
For several generations Columba House has been a magnate for international as well as British scholars and knowledge about Scottish Catholicism has grown apace.
But this work is being torn up by Archbishop Emeritus Mario Conti, for 35 years a bishop first in his native Aberdeen and later in Glasgow. This consummate church politician has a legacy project and, it seems, will brook no opposition in order to secure it. He wants to create a Catholic hub of learning and culture at Aberdeen University, which has agreed to house up to one million items from the Edinburgh archives for the period before 1878.
He won round fellow prelates who had either forgotten why Gray had unified the archives or else were persuaded that the Church’s money troubles could be eased by this controversial move.
The Catholic Church may be a hierarchy, but today’s ageing bishops only hold these archives in trust and their governance is shared with lay organizations such as the Scottish Catholic Heritage Commission. Conti has simply frozen out the other parties.
In the autumn of his life, this still-energetic prelate is running an important dimension of the Scottish Church as if it were an investment bank. It seems as if his own status and desire for a legacy trump any duty of care towards precious church artefacts and their accessibility to scholars and the wider public.
In May 2012, 90 historians signed a letter of protest deploring his actions. But even as scandal engulfed the Church on several fronts, no bishop had the resolve to call Conti to heel and mend fences with scholarly men and women normally well-disposed to the church.
Respected archivists were got rid of and from last October, Columba House was boarded up for long periods in preparation for the move north.
But in December it was discovered that rampant mould had seriously damaged large numbers of documents.
This summer the Scottish Parliament has been approached by professional bodies which the Church, in less unhinged times, used to collaborate with, in the hope that Holyrood can avert "a cultural catastrophe".
These are the words of Dr Michael Turnbull, Cardinal Gray’s biographer and an Edinburgh-based historian who has been indefatigable in publicising what has been going on.
After the signatories to a petition had been advised by parliamentary officials to "involve sympathetic MSPs directly, rather than invoking the public petitions procedure", he wrote to his local MSP, Labour’s former leader in Scotland, Iain Gray, and he is awaiting a response.
However, the Culture Minister, the SNP’s Fiona Hyslop, has refused to intervene.
The SNP has long cultivated church leaders and years ago managed to entice Cardinal O’Brien on board its independence charabanc.
In April at Margaret Thatcher’s funeral, Alex Salmond displayed the customary indulgence that he has for any Scottish institution, however well or badly run, as long as it dances to his tune – he insisted that the Catholic Church would recover from its current troubles and remain at the centre of Scottish life.
Perhaps it is only intervention from Rome that can halt the damage being caused by a small number of high-placed clerics in Scotland.
But will Pope Francis have the time and inclination to show any interest?
If not, however gifted and principled the prelate who succeeds Keith O’Brien in Edinburgh proves to be, his efforts are almost certain to be dogged by this act of episcopal vandalism.
Some of the loudest laughs are sure to come from those radical secularists who wish to weaken Catholic schools through passing a law that requires children to opt in for religious education and teachers to be sacked if they question the value of same sex marriages.
Scotland’s bishops are fast running out of allies as they persist in alienating Catholic intellectuals and professional people by their crass conduct.
In writing a book Divided Scotland: Ethnic Strife and Christian Crisis which Argyll Publications will publish in a few weeks, I have found it hard to find a similar example of collective abdication from responsibility by church leaders than this one.
Perhaps the best step Pope Francis could take is to unify the Scottish Church with its nearest neighbour, that of England and Wales.
It is likely that Scotland’s religious patrimony would be better protected under a Filipino or a Peruvian, or indeed someone like the Yorkshireman Charles Eyre who was the first archbishop of Glasgow when the Catholic hierarchy was restored to Scotland 135 years ago.