The row over the Speaker’s decision may look like a particularly indulgent form of deckchair rearrangement. But in parliamentary terms it is historic. And whatever form Brexit finally takes, it will be part of the shape of the Britain that emerges.

On Wednesday morning John Bercow was widely reported to have ignored the considered advice of the official guardians of the rules of procedure, and allowed a cross-party amendment tabled by Dominic Grieve to be voted on.

The amendment, which was passed, forces the prime minister to come back within three sitting days if her withdrawal agreement is voted down, rather than the three weeks imposed by an earlier Grieve amendment. Its backers say it just puts the timetable back where it would have been if the prime minister hadn’t ducked the vote before Christmas. It would open up the possibility of a proper debate about what to do next. But should the Speaker have let the vote happen at all?

The rules that govern debate and law-making in parliament are theological both in their density and history. For those who think in such terms, they are the nearest thing to a written constitution that Britain has, and the clerks, the men and women whose job is, among other things, to make sure the rules are observed, have a certain priestly status.

First elected when parliament’s reputation was at its shabbiest in the aftermath of the expenses scandal, Bercow has done a lot to enhance the powers of backbenchers. Two long periods of governments with big majorities and big reform agendas had eroded the devious tactics used by wily MPs and well-organised oppositions to slow headstrong ministers. Bercow’s championing of backbench rights has earned him the support of many MPs, which has seen him through some recent times when his hold on power has looked downright shaky as allegations of bullying (which he denies) pursue him.

Margaret Beckett, the former Labour cabinet minister, may have been indiscreet when she said she’d back him despite the bullying allegations because he’d be a useful ally in the Brexit battle – “if it comes to the constitutional future of this country, the most difficult decision we have made, not since the war but possibly, certainly in all our lifetimes, hundreds of years ... it trumps bad behaviour” – but she was only acknowledging what everyone already knew: the Speaker, supposed to be a pillar of impartiality, was a remainer.

Bercow is not the first Speaker to make a unilateral change to the parliamentary rules. But it would be fair to say it doesn’t happen often. Experts who know their history point to the power to shut down debate (“a closure motion”) which was introduced by Speaker Brand after Irish MPs stopped all progress on a government bill for five days in a row. That was in 1880, approximately 140 years ago.

But the real point about Bercow’s actions is the furious accusations of party bias that it has provoked from his critics. “The political impartiality of the Speaker is a key feature of the office, while the role’s authority has developed over time alongside other procedural reforms” intones the Commons guide to the office of Speaker. It’s one thing to stand up for backbenchers against a powerful executive. It’s quite another to use the office to advance a political cause.

In the end, the judgment will rest on whether the failure of government and parliament as a whole to find any grounds for agreement on Brexit legitimises intervention on one side by the Speaker – or whether instead it marks a wanton disregard for the rule of law. Everyone knows where unchecked law-breaking can lead. The Speaker takes a grave risk when he appears to ignore the rules. At the least, it makes it harder to insist the government observes the rules next time.

Everyone who is fighting to reverse the decision to leave the EU because it is a wanton act of self-harm has a parallel duty, to ensure that it is done in a way that promotes rather than undermines democracy. Brexit is already doing terrible damage, and it’s not all on one side. The Speaker should be very careful of doing anything to make it worse.