However, his unexpected departure has left behind a chill wind of change blowing through the organisation, an unwelcome legacy for those working in the BOA's headquarters in London's Charlotte Street, where chief executive Andy Hunt has embarked on a cost-cutting exercise that could see some losing their jobs.
But in moving so hastily to push through his restructuring plans before the anticipated accession of Lord Coe to the chair, Hunt may well have has put his own role jeopardy.
Coe will be annoyed to learn that as part of the slimming down Hunt apparently intends to axe director of performance Sir Clive Woodward, a figure he much admires and would wish to retain in some capacity, and implement other changes before he stands for election on November 7. The 2012 supremo, who is expected to succeed Lord Moynihan despite a possible challenge from British Hockey chief Richard Leman, is keen to be involved in any shake-up at the BOA but has not been consulted on Hunt's blueprint for rationalisation, which includes merging some top jobs and shedding others up and down the line.
Significantly Hunt, hired by Moynihan from the commercial world to succeed Simon Clegg before the Beijing 2008 Games, strongly resisted attempts to bring forward the election date, thus getting Coe in situ sooner, and is believed to be among those who have urged Leman, a close friend of Moynihan, to stand against him.
If Coe wins, it seems doubtful that Hunt will stay, with Coe looking to earmark Woodward as Chef de Mission for the Sochi Winter Games in 2014 and Rio's 2016 Summer Games, a part-time appointment that would reduce the BOA's hefty wage bill and leave the former England rugby coach free to pursue other lucrative media and sporting interests.
There was great regard for Woodward's liaison role with the athletes as deputy leader to Hunt during 2012, less so for Hunt's, his daily deluge of social media cheerleading parodied by the Twitterati as the work of "Randy Shunt".
In retrospect, Hunt's insistence on being an up-front Chef de Mission – a function he also performed in Beijing and Vancouver – might be viewed as a misjudgement.
You can't be both anchorman and midfielder, as Moynihan himself had intimated when suggesting that even Bill Gates would have found it virtually impossible to fulfil dual roles of Chef de Mission and chief executive at a London Games.
I believe Moynihan was also surprised by Coe's acceptance of the nomination to follow him. "I wouldn't think he'd be interested," he said shaking his head when I asked him about this possibility at the Cinnamon Club lunch he gave the day after the Olympics to announce he was stepping down.
Interestingly Leman, a British hockey gold medallist and BOA board member, was one of his guests, as was canoeing's Albert Woods, a BOA vice-chairman.
Both were also nominated, but Woods has now withdrawn. As far as we know, Leman continues to stand.
The initial candidate selection, organised by head-hunters Odgers Berndtson, who widely advertised the unpaid post, closed yesterday, but the BOA have until October 7 to receive other nominations from within the organisation.
While obviously Coe would prefer to have a clear run, it is thought that there are constituent members of the BOA who are concerned he would be using the position as a promotional platform for his bid for the bigger prize of the Presidency of the IAAF in 2015.
Their preference could be for someone who currently leads a national sporting body – like, Leman, or rowing's Di Ellis.
There is also another possible scenario: that Coe may be unwilling to contest an election, and backs out.
One hopes this will not be the case because domestically and internationally he is the ideal figurehead to carry Olympism forward after London covered itself in such glory.
Moreover, he is the one person who might facilitate a vital handout for the BOA from his close friends in Government.
Because assuming he does take control, he will inherit a financial situation that is far from healthy, with the BOA heading for an anticipated post-Games deficit of some £2 million ($3.2 million/€2.5 million).
Further bad news is that London 2012 is expected to break even when the accounts for the operation of the Olympics and Paralympics are finalised which means there is unlikely to be an money left over, a blow for BOA, which would be entitled to 20 per cent of any profit from the running of the Games.
The share of any surplus was the cause of an acrimonious legal dispute between the BOA and London 2012 last year – the BOA unsuccessfully claimed the running costs of the Paralympics should not be taken into account.
Instead, London 2012 gave the BOA the rights to sell an "iconic" item of merchandise – the BOA chose branded scarves and collectable medallions available from petrol stations, but sales of these fell far short of expectations.
The spat marked a low point in relations between Moynihan and Hunt and the London 2012 leadership. If there is to be no surplus, it will go down as a costly and ultimately pointless episode.
The departure of Woodward, on a reputed salary of £300,000 ($500,000/€400,000), would represent a considerable saving for the BOA, as does that of communications director Darryl Seibel, who is returning to the United States next month at the end of his contract after heading up a Games media operation as professional and efficient as any I have experienced in international sport.
Commercial director Hugh Chambers is also said to be under threat as Hunt attempts to shore up his own position while clearly on a potential collision course with Coe, who understandably would want to be involved in any reorganisation.
If Hunt, currently in Rio seeking an early GB preparation camp does go, the UK Athletics chief executive Niels de Vos would be high among those on Coe's list as a replacement.
By curious coincidence, Clegg, Hunt's predecessor, who was never known as an axe man during his own BOA tenure, finds it a role he has had to adopt in his new guise as chief executive of Ipswich Town FC.
Having already fired two managers, Jim Magilton, and somewhat bravely, Roy Keane, it seems Clegg may be on the brink of his hat-trick, with luckless incumbent Paul Jewell admitting he may be for the chop with the club languishing in the foothills of The Championship.
Rumour has is that Harry Redknapp is being lined up to take over at a salary, one imagines, considerably more than Woodward's.
Meantime as he awaits the outcome of the political in-fighting, Woodward himself is on the mat – the judo variety. He is chairing an independent review into the future of a sport, which was saved by the belles in the London Games, the first Olympic medals in 12 years being won by Gemma Gibbons and Karina Bryant.
As at the BOA, an election for a new British Judo Association (BJA) chair is pending with Densign White, husband of Tessa Sanderson, standing down.
He had been accused of "rotten leadership" by veteran Olympian Winston Gordon after criticising the commitment of some of the athletes.
Woodward has been asked to conduct "a root and branch review" of how to find future Olympic medallists, heading a panel, which includes former Football Association chief executive Mark Palios and top judo coach Roy Inman, who is also standing for the BJA chairmanship.
A more controversial candidate is Kerrith Brown, who was stripped of the bronze medal he won at the Seoul 1988 Olympics after testing positive for the use of a banned substance.
Funding body UK Sport is known to be keeping a watching brief on the election and if not satisfied with the outcome could refer it back to the BJA and suggest they seek an independent chair, as they did with fencing. Is this something Woodward himself might get to grips with?
Alan Hubbard is an award-winning sports columnist for The Independent on Sunday, and a former sports editor of The Observer. He has covered a total of 16 Summer and Winter Olympics, 10 Commonwealth Games, several football World Cups and world title fights from Atlanta to Zaire.