On one level, the argument about what Sir Simon McDonald said to the foreign affairs select committee this week can be dismissed as a storm in a Whitehall teacup. Hours after the head of the foreign office had called Britain’s refusal to join the European Union’s procurement efforts during the Covid-19 pandemic a “political decision”, McDonald retracted his words. Whitehall-watchers are fascinated. The wider world has bigger things to worry about.

But on another level, this week’s row is political dynamite – and for two main reasons.

First, and more immediately, the McDonald affair is another challenge, this time from the Whitehall high command itself, to the government’s increasingly desperate attempts to show that ministers have successfully gripped the effort to secure life-saving medical equipment and protective kit for the fight against the virus. At its most serious, it comes down to an admission that ministers who previously said that the UK did not take part in the ventilator procurement programme because of “communication” errors were actually in a position, early on in the pandemic, to save more lives by joining the scheme, and yet deliberately chose not to.

Second, Tuesday’s furore shoots a beam of light into the dark and tangled argument at the heart of British politics about the longer term strategy and objectives of Boris Johnson’s government. It is a reminder that, in this government, power still rests with those who believe the overriding objective of this administration, even now, is a hard Brexit. It implies that in Johnson’s government the fight against Covid-19 is, of course, massively important – but only up to a point.

McDonald’s session with the foreign affairs committee was not, at the outset, about participation in the EU procurement programme at all. Most of the first hour was about efforts to repatriate UK nationals from around the globe. But when, later on, the committee chair, Tom Tugendhat, asked whether Britain’s failure to take part in the EU programme was a political decision, the head of the foreign office confirmed that it was.

The hasty retraction letter on Tuesday evening was extraordinary. If nothing else, it confirms the incredible sensitivities in government at the moment about its handling of the pandemic. The letter also needs to be read carefully. The key sentence nevertheless appears to be this one: “Ministers were not briefed by our mission in Brussels about the scheme and a political decision was not taken on whether or not to participate.”

The more you read the letter, the more questions it raises. The key point is that, in early February, while the UK’s Brussels mission did not brief ministers – the denial in the letter – about the EU scheme, the Brussels mission clearly did brief departmental civil servants. In practice, that means that Brussels briefed the Foreign Office and the Department of Health and Social Care about the ventilator procurement scheme, presumably at a senior level, in detail and as an issue requiring priority attention. Those civil servants will then have briefed their ministers, including the foreign secretary, Dominic Raab, and the health secretary, Matt Hancock. So ministers were indeed briefed, only not by “our mission in Brussels”. In other words, the ministers knew about the scheme and knew they could take part in it.

What exactly happened next depends in part on what is meant by a “political decision”. That phrase has now been denied. But it is hard to take the retraction too seriously, other than as a means of removing ministerial fingerprints. It can mean what many people would assume, that the decision was political rather than practical or commercial. But in civil service-speak, a political decision can also mean a decision taken by ministers, who are political, rather than officials or expert specialists, who advise them about it.

In this context, that would most probably mean the decision, even in the shape of a “non-decision” to let the issue lie on the table, was taken by or on behalf of Boris Johnson in No 10, but it would be essentially political in both senses. That seems to fit with other evidence suggesting that the question was indeed discussed at Cobra meetings, which always report to the prime minister. It would also be valuable to clarify how and in what terms that initial decision in London was then communicated in a response to the EU in Brussels. If London chose to write itself out of the EU process in February, that may help explain why the UK claims not to have been informed about other joint schemes later.

Even without the full details, there is no way of reading these events as anything except another, and early, example of the government’s failure to take Covid-19 seriously enough soon enough. More than two months later, in Raab’s words in the Commons today, it is now the government’s official policy to take “the right measures at the right time, guided by the science and the medical experts”. But this was not true in February, when the science and the experts were ignored at Cobra. Instead, the decision not to join the EU efforts has contributed to the shortages and failings on which Keir Starmer began his parliamentary career as Labour leader today.

But the importance of the decision goes further, and in a direction that Starmer chose not to follow, perhaps wisely on his debut. The political decision not to join the EU procurement process reflected what was uppermost in Johnson’s and other minds in February. Britain, as McDonald stressed this week, had left the EU on 31 January. The Brexiters had done what they promised at the election. The national ship was being set on a course that turned its back on Europe. They weren’t interested in new post-Brexit links with EU schemes any more than they were interested in establishing such links during the transition period.

Any suggestion, at this of all moments, that the UK should opt into an EU scheme on anything will have been dismissed with contempt. It was in every way a political decision. A month or so later, things – including politics – were different. When Hancock was offered a renewed chance to join another EU-wide scheme, the offer was taken up. But by then Covid-19 was a far larger reality, the UK was facing lockdown, and ministers were playing catch-up, just as they still are today.

McDonald’s retraction on Tuesday shows that, even in the face of Covid-19, not as much has changed as some might assume. The retraction is not just a partisan correction of the record. It is a statement that the Johnson government will maintain its ideological opposition to anything except a hard Brexit. Those who say, as David Lidington did this week, that a Brexit extension is now inevitable because of Covid-19, may be deceiving themselves.

In this government, especially as it struggles to control the coronavirus outbreak in the face of shortages and deaths, the pandemic remains an all-consuming but still essentially temporary concern. Johnson’s essential project is not to save and rebuild the nation. It is Brexit. Always was. Still is.

• Martin Kettle is a Guardian columnist