Observers of the European referendum debate may be a tad puzzled by Nicola Sturgeon’s continuing enthusiastic backing for the remain cause, when Brexit would seem to better serve her primary political goal of Scottish independence.

On Tuesday she went where other pro-Europeans have feared to tread, overtly linking the killing of Jo Cox MP to a growing sense of public disgust over Nigel Farage’s “Breaking Point” poster and the “poisonous” nature of his referendum campaign.

But the Scottish first minister wasn’t as keen to insist that a Brexit vote would be an automatic green light for a second Scottish independence referendum: “I want Scotland to be independent but I wouldn’t choose to have that happen because England votes to come out of the EU.”

Why not?

Scots have been leaders of the pro-European pack since the referendum was announced with remain polling a steady 20 percentage points ahead of leave. There’s a wheen of reasons for that; the warm afterglow of being a net recipient of EU funds; the even warmer memory of EU regulations acting as a shield against the worst excesses of Margaret Thatcher; a smaller minority ethnic population, a lower rate of immigration and cross-party consensus in Holyrood that Scotland needs more migrants not fewer and distaste for the little Englander presumption that British culture is infinitely superior to any other.

But one of the biggest reasons for the pro-European stance north of the border was the independence referendum during which the “danger” of being kicked out of the EU was one of the biggest arguments against a yes vote in Scotland. Many commentators suggested a Tory general election victory would pose a bigger threat, and voila, here we are. But for two long years in Scotland the question about EU membership was never whether it was desirable – only whether it would be possible after independence. The presumption of desirability has stuck.

No Scottish party leader is pro-Brexit. Only two members of the new Scottish parliament are pro-Brexit. Former SNP deputy leader Jim Sillars backs leave on the grounds that EU powers over agriculture, fishing and the environment would be repatriated to Holyrood not Westminster. But powers are not the same as money and few Scots believe the UK government would play fair with either.

So Scots are fairly pro-Europe but not that excited about the issue. There are no posters in windows and turnout could be low. That’s partly why Nicola Sturgeon has hedged her bets. It would be a mistake though to think lethargy before the vote will mean apathy after it. Waving a tearful farewell to Brussels may not fire up Scottish independence campaigners, but the prospect of being governed by Lord Farage (when Ukip polled about 2% in the Scottish elections) alongside prime minister Boris Johnson certainly will.

No matter how often David Cameron insists he will tough out a Brexit vote as prime minister, a change of leadership in the Tory party and therefore the UK government is inevitable. That prospect will strike fear into the heart of progressives across Britain, but it will be the final straw for many voters in Scotland. Not only will progressive, pro-European Scots find themselves out of Europe against their will, they will also find themselves governed by a rabble of rightwing extremists, none of whom would have the slightest chance of being elected in Scotland.

Of course in the recent elections here, the Conservatives did overtake Labour to become the official opposition and that’s prompted some to speculate that Scots have reached “peak SNP”. But the Tories’ success only confirms that the biggest dividing issue in Scottish politics is now the constitutional question and the Tories formidable Scottish leader – tub-thumping, outspoken Ruth Davidson – is seen as a more effective champion of the union by many no voters than Labour’s relatively low key Kezia Dugdale.

But make no mistake. Ruth Davidson didn’t win second place as David Cameron’s wee Scottish helper. Au contraire, she won by keeping Cameron, Osborne et al at bay. Now “sources close to the Scottish Tory leader” say she thinks the Scottish Tories will have to break away from the UK party and campaign under a new name if Boris Johnson succeeds David Cameron in the wake of a Brexit vote. Davidson denies this but did say Johnson has the same “brazen chauvinistic style” as Alex Salmond in a recent newspaper article. But one thing’s certain. If the Scottish Conservatives have even considered going their own way in the event of an ultra-rightwing Tory party takeover, the union is doomed. Because at long last, the main defenders of the union have acknowledged that Scotland’s distinctive political culture doesn’t fit inside British political structures.

This would obviously help the case for a second independence referendum but it wouldn’t produce Nicola Sturgeon’s ideal indyref2 scenario – the possibility of a “hard border” between EU member Scotland and non-member England wouldn’t help either economy and the current low oil price doesn’t make for an easy economic argument.

Besides, aged just 45, the Scottish first minister has enough time and experience to wait until distaste, anxiety and disbelief in the actions and personalities of a Boris Johnson-led government combine to persuade wobbly no voters that independence is now a relatively safer option than continued membership of the splendidly isolated United Kingdom.

That won’t happen on Friday. But it will happen soon.