The change cost hundreds of thousands of pounds; symbolically, and most embarrassingly, a design consultant charged pounds 30,000 to come up with a logo resembling a suspension bridge, notionally based on the Scales of Justice. Mr Boateng made sure the costs were publicised.
It was an inauspicious start for Michael Huebner, 54, educated at Rugby and Oxford, called to the Bar in 1965, and a career civil servant since then in the Lord Chancellor's Department, and still tipped to become its next permanent secretary in 1997.
Mr Huebner, though, has no difficulty defining the purpose of the switch to agency status: "It's about separating the management of Court Service from the policy and other functions of the [Lord Chancellor's] department. The job I now do used to have quite a lot of policy functions ... It has now been distilled into chief executive and nothing else.
"The whole agency concept gives us a being of our own, still within the department, effectively with total control of the relevant budgets." He is answerable directly to the Lord Chancellor, rather than the permanent secretary.
All this is important to him, and to long- and short-term management, but the most tangible change for the "consumer" could have happened under the old structure. Significantly, despite the obvious need, it never did. Now, however, since it achieved agency status, the Treasury has allowed the service to spend money under the Private Finance Initiative on computers to bring the civil courts out of the paper-shuffling pre-war ethos, and into the modern information technology world that banks, building societies and big law firms entered in the early Eighties.
Three firms are already tendering for the work, and the winner will be announced in May. The firm should then form a relationship with the Court Service and work towards further improvements. In return for the pounds 60m- pounds 70m cost of the initial stage, the taxpayer will get a listings service linking every county court, an on-screen update of the progress of cases, automatic reminders to parties, and maybe later a link to solicitors' offices. The partnership with the computer firm will then embrace the technology needed to make Lord Woolf's proposed civil justice reforms work, by allowing judges to manage cases more effectively. The High Courts have to be included at some stage.
There is a huge management problem with trying to anticipate Woolf - no one knows exactly what it will recommend next year, or how much of it the Government will accept. Everybody knows the changes would make the courts cheaper to run by eliminating waste at all stages.
But most people in the legal professions expect there to be an initial cost to fund pump-priming - in other words spending now to save later. That is improbable for an increasingly wobbly Conservative Party, which would be unlikely to favour spending ahead of the election to gain benefits that would only flow afterwards, possibly to Labour.
Mr Huebner, with the independence and control that agency status gives him, is optimistic the budgets can be juggled to find the money to spend without the total going up. And the juggling act has to include the political uncertainty as well as the budgets. Again he is confident: "There is a big thrust for change here, and this we're recognising. Work is going ahead without the final decisions being taken. It seems very likely we will move down that road." He meets Lord Woolf and the Lord Chancellor's aides frequently, so his prediction should be taken as more than just a guess.
One of the hopes, or fears (depending on political orientation), of the creation of agencies was that they would bring a new vibrant management culture, embracing efficiencies, savings and job losses. Mr Huebner is equivocal: there will be rationalisations and reorganisations, but there would anyway; computerising the county courts equates to 600 job losses; some people may be redeployed to new work demanded by the Woolf proposals rather than lost. Overall, he says: "We're going through a fairly painful look at how we manage ourselves, and we're likely to emerge in a year or so's time at a structure with fewer layers of management with fewer duplications."
The agency will develop different conditions and gradings from the Civil Service, but Mr Huebner wants to keep the terms sufficiently similar for staff still to be able to transfer from one to the other.
Mr Boateng and others have warned of a constitutional threat from tension between the Court Service, with its targets for efficient use of courts, and some judges, who tend to let cases run inordinately long in the interests of perfect justice. Mr Huebner sees no difficulty: if there is a judge who is too slow, that is for the Lord Chancellor's Department and the senior judges to sort out: "Some judges clearly work more quickly than others; they work in different ways; this is part of the system we accept and support. There are no problems there," he says.
It will be interesting to see what happens to that analysis in the longer term as targets for the Court Service become more difficult to meet. There is another area - costs charged to court users, where the change to agency status is set to explode embarrassingly in the Government's face.
At present, quite a lot of users of the court system are chain stores issuing summonses for debt recovery. Under the system the user pays at the start of the proceedings for issuing a summons. Plaintiffs who accept a settlement without the case coming to court are subsidising the few, often ordinary, individuals whose hearings carry on for several days.
But Mr Huebner wants to remove cross-subsidies, and introduce daily fees. He will propose this to the Lord Chancellor in January. Figures of pounds 200 a day for county courts and pounds 500 for High Courts have been mooted.
"I believe a system whereby you pay a fee for what you are going to get without subsidising other people is likely to lead to a better managed civil justice system, and to put either encouragements or constraints on people via the fee system at the right places."
The Court Service now recovers about 75 per cent of the full cost of civil justice, and the Government is committed to full recovery. " From my own point of view as chief executive it's quite important to have a system like that because it enables me to plan better for our fee recovery."
The Government either replaces the subsidy with taxpayers' money, or it lets the fees go up, and faces howls of anguish that it has restricted access to justice. It might be rational, but it will be a political nightmare either way.
But Mr Huebner the civil servant was there to serve the Lord Chancellor; Mr Huebner the agency head is there to look after the courts. The problem of court fees is one of "policy", and as he points out, "policy" is the part of his job he has shaken off. "I regard that as a general policy question far above my head."