When a team from football’s third tier knocks one of the game’s giants out of a cup competition, it’s usually seen as a good thing by all but fans of the vanquished and embarrassed losers. Unless the team doing the giantkilling is MK Dons.

The fact that this week’s 4-0 victory over Manchester United by MK Dons did not spark universal joy prompted some to ask whether too many football fans were stuck in the past; whether begrudging the side dubbed Franchise FC their achievement was a little mean-minded. MK Dons won the game fair and square and, what’s more, say the pragmatists, they are a club with an impressive youth policy and one which does a lot of good work in local schools. Surely it’s time to forget about a dispute that happened ten years ago?

It seems a reasonable point. But making the point risks underestimating the resonance of what one football industry insider described to me as “the biggest single governance failure in English football” – the decision in 2004 to give the old Wimbledon FC’s place in the league to a newly-formed club. A decision which then-Football Association chief executive Adam Crozier described at the time as “appalling”.

To understand the strength of feeling over the issue, imagine how it would feel to have the club you support stolen from you, relocated, renamed, made into something entirely different. Talk to most fans of the old Wimbledon FC and they will describe what happened in exactly those terms.

Wimbledon FC was relocated from south west London to Milton Keynes against the wishes of a large majority of its fans in 2002. The move was also opposed by the FA and by the Football League, which said any new club in Milton Keynes would need to gain league status by progressing up the pyramid just as other clubs did. But the FA then set up an independent – but hand-picked – three-man commission to decide on the move, and it was approved to general astonishment on 28 May 2002. The decision was final and binding.

It’s important at this stage to understand the background to why a football club was needed in Milton Keynes. Asda, the world’s largest supermarket chain, wanted a presence in a Tesco stronghold and wanted to build Europe’s largest supermarket there. Planning rules meant that development on greenfield sites was not supported, but the proposed MK Asda would not work on a brownfield site.

The only way the greenfield site restrictions could be got around was through what’s called “planning gain” – in plain English some demonstrable benefit to the local community that would come from allowing development. A football stadium would be one example of a civic amenity that would do the job. But Milton Keynes did not have a team that needed a stadium on the scale required. And with no team, there would be no stadium, and therefore no development.

And so the Milton Keynes Stadium Consortium, led by pop music entrepreneur Pete Winkelman and supported by Wal-Mart subsidiary Asda and furniture giant Ikea, began to look for a football team that could occupy the 30,000 capacity stadium needed to enable the development of the retail, hotel, stadium and conference centre development they wanted to build.

Luton Town, Crystal Palace, Barnet and QPR were approached, along with Wimbledon. At one stage, a merger of QPR and Wimbledon was mooted, prompting fierce opposition from fans of both clubs. The consortium appeared to be getting nowhere. Then, in 2001, Wimbledon FC owner Charles Koppel announced the club would be moving to Milton Keynes, setting in motion the process that eventually led to a decision opposed by almost everyone concerned, including the bodies that were supposed to run the game but which could apparently not enforce their own wishes.

Most fans of Wimbledon FC viewed this as the theft and destruction of their club, and founded their own team, AFC Wimbledon, which began to work its way up from the bottom of football’s pyramid system. Wimbledon FC, meanwhile, struggled on and off the pitch, being relegated and going into administration at the end of the 2003/04 season. With the club out of business, the property development project was threatened. So Winkelman brought Wimbledon FC out of administration in June 2004, renamed the club Milton Keynes Dons, and changed the colours and badge. But the choice of Dons, the nickname of the old Wimbledon FC, the basing of the new badge on the old crest, and Winkelman’s insistence that the new club was the “real child of Wimbledon”, rankled.

The ensuing dispute became bitter. Winkleman responded to criticism by accusing AFC Wimbledon’s fans of “betraying” their former club, and said they “abdicated their right” to the club’s history “when they walked away”. In 2006, after prolonged negotiations, MK Dons renounced any claims to the history of Wimbledon FC before 2004. In return, the Wimbledon Independent Supporters Association agreed to drop calls for a boycott of MK Dons games.

And that, say the pragmatists, is that. Surely it’s time to let bygones be bygones. But, as one AFC Wimbledon fan told me: “It’s grubby, and what sticks most is that MK continue to deny all of that ever happened. In their narrative, Wimbledon was dying, the fault of the fans in south west London, and they saved it. In their narrative, they’re the good guys and we’re the bad guys. It’s hard to feel equanimous towards people who think they’re the victims.”

And in response to the point that, now AFC Wimbledon have gained a place in the league the proper way, on playing merit, surely it’s time to let it all drop, he says this. “That’s like saying that a person who has the car they build themselves nicked should get over it because they managed to build themselves a new car instead, despite the person who nicked their car having pimped it, blamed the person who built it for the theft and then driven all over town with the sunroof down like the big I am.”

It may be easy to dismiss such arguments as emotional, but football trades on emotions, and the issues raised by the murky story of the origins of MK Dons strikes at the heart of valued notions of community, continuity and fair play. And there are important considerations beyond those no less important emotional ones, too.

The industry insider I spoke to said the decision to allow the relocation “was the high water mark for attempts to paint football as some sort of free market” which “made it possible for others to do similar things”. The current goings on at Coventry City provide a good example. That 2002 decision also “chipped away at part of the foundations of what clubs are” and puts the consortium of private companies behind MK Dons into the middle of football’s decision-making process.

It’s legitimate to ask why, if you are an ambitious manager, a young player, or even a young fan in a town wanting to support your local team, you should be expected to atone for sins committed a decade ago indefinitely. Outside of the complex emotions of football, it must seem rather curmudgeonly to perpetrate the resentments of yesteryear.

But football is what it is because of those complex emotions. The existence of MK Dons remains a challenge to the values that make the game the emotional and therefore commercial property it is – the result, let’s remember, of “the biggest single governance failure in football” in one insider’s opinion. So what would move things on? Perhaps acceding to the demands of the Wimbledon Guardian’s campaign calling for the Dons part of the MK club’s name to be dropped would help. Better still, a genuine recognition of what was wrong with the process that led to the establishment of the MK club and a proper commitment to stop anything like it happening again.

It is possible to look at the achievement of MK Dons’ manager Karl Robinson and his team this week and salute the achievement, to recognise a famous victory achieved fair and square. But already there are signs of the club’s hierarchy using the platform the victory has provided to normalise a situation that many believe should not be normalised, to gloss over the past and to entrench the victim-blaming that has so enraged fans of the real Wimbledon over the years.

And that’s why this week’s giantkilling has not prompted universal joy.

Martin Cloake’s latest book, Taking Our Ball Back: English Football’s Culture Wars, includes a selection of his writing from the New Statesman website