The abrupt withdrawal of Frank Flannery’s Dáil pass and his departure as director of elections for Fine Gael in the forthcoming local elections illustrated the old cliché that politics is a cruel trade.

Flannery has been a key figure in Fine Gael going back to the early 1980s when he was one of a group of unpaid advisers dubbed “the national handlers” who helped Garret FitzGerald remodel the party.

In more recent times he was a central figure in transforming Fine Gael from a badly beaten and demoralised organisation after the crushing defeat of 2002 to becoming the biggest political party in the country in 2011.

The Flannery Report commissioned by Enda Kenny in the summer of 2002 provided the blueprint for recovery. It was crucial in helping the widely underestimated Kenny defy the pundits and become the most successful Fine Gael leader in the party’s history.

Despite his importance to Kenny and Fine Gael, when he became a political liability last week there was no room for sentiment and Flannery was cut loose.

Winston Churchill in his book Great Contemporaries quoted an adage of another great British politician ,William Ewart Gladstone, who once remarked: "The first essential for a prime minister is to be a good butcher."

Churchill noted that at certain times, when the public need required it, political allies had to be put aside once and for all. “Personal friendship might survive if it would. Political association was finished. But how else can states be governed?”

Flannery became a political liability for the Government over the past couple of weeks because of his poorly judged response to the unfolding inquiry by the Public Accounts Committee (PAC) into the charity sector.

Since the economic crisis struck in 2009 hardship has been endured by a range of groups and individuals across Irish society. The necessary squeeze on public spending has resulted in pay cuts across the public service as well as the job losses and pay cuts in the private sector.

It was inevitable and appropriate that at some stage the State’s allocation of more than €3 billion a year to the charity sector should be put under the microscope.

Exchequer-funded salaries right across the board from politicians and senior public servants to quango and charity chiefs were allowed to spin out of control as a result of the disastrous “benchmarking” exercise. Most have been cut back since austerity struck, but it is only now that the funding of the voluntary sector is really getting the attention it deserves.

While the bulk of the €3 billion for the sector goes to fund vital services that benefit the truly vulnerable people in Irish society, the pay of those working in the sector is largely funded by the exchequer grants and there has been growing concern about the large salaries of some of those in leading positions.

The Health Service Executive has rightly been looking into how exchequer funding is being spent and that in turn has triggered the investigations by the PAC into the pay scales of people at the top of organisations such as the Central Remedial Clinic and the Rehab Group.

Both organisations have an untold amount of good work over the years. Rehab first under Flannery’s leadership and more recently that of Angela Kerins developed into a large organisation that employs 2,470 staff in Ireland and 3,500 in total across its operations which also cover England, Wales, Scotland, the Netherlands, Poland and Saudi Arabia.

In the statement during the week detailing its pay scales, the organisation pointed out the kind of services it provides for people with physical, sensory and intellectual disabilities. More than 60,000 people and their families benefit from the supports provided by Rehab in more than 260 locations and group had a turnover in 2012 of €183 million.

The problem is that the pay of its senior executives is high by any standard, with the group chief executive Kerins being paid about €240,000 a year which is €40,000 a year more than the Taoiseach. Her initial refusal to disclose her salary focused political and media attention on her appearance at the PAC. That in turn put the spotlight on Flannery, who is still a member of the Rehab board, particularly as he turned up in the corridors of Leinster House on the day she gave evidence but did not appear at the committee.

He was widely criticised for not appearing to give evidence at the PAC although it has since emerged that he was never invited. He has now said he will appear to answer questions if he is formally asked and if the committee indicates what it wants to question him about.

Flannery’s problem is that his highly publicised visit to Leinster House on the day Kerins appeared focused attention on his unrestricted access to the Dáil and his lobbying activities.

There was surprise among politicians when it emerged in The Irish Times last week that he was being paid by Rehab to lobby on its behalf. That in turn put the focus on his role not only in Rehab and its commercial activities but also on lobbying on behalf of Philanthropy Ireland.

Labour Minister for Education Ruairí Quinn raised the political temperature by disclosing that he had been lobbied by Flannery in the Leinster House corridor where all the Ministers have their offices, before Cabinet meetings.

Flannery had access to the corridors of power because he had accreditation as a member of the Fine Gael political staff. That raised all sorts of questions about the appropriateness of his lobbying, even if it was for a charitable organisation.

On the wider political front the more damaging fallout from the affair is that it appears to show Fine Gael in acting just like Fianna Fáil used to do when it controlled the levers of power.