The issue is whether Scotland will leave the UK. Scotland is the member of the UK by reason of Scotland's Union with England to form Britain in 1707. Nobody argued about the N Isles then.
As stated, this is simply the normal imperialist mischief seen in Ireland and India and Palestine. But these days have gone my friend. The Scottish government governs Scotland, not bits of it. All of it within the areas of autonomy it has received. And that's not imperialism, but governance. In a future independence referendum some parts of the country will vote yes and other bits will vote no. But the fate of the country as a whole will be determined by the majority. Bits of England voted different ways in the EU referendum. Is it intended to allow Brussels to cut England to pieces with a fret saw because of that? Nonsense. It all goes or all stays in the EU. Scotland will have a referendum and all go, or all stay in the UK.
My part of Scotland voted Yes in the 2014 referendum, but I don't think Scotland should be cut to bits to accommodate the wishes for independence of the local majority in this area. Neither do you. This is all nonsense intended to boost the Union.
But regarding
this, surely you can see that one could use precisely the same argument to state that
the UK Government governs the UK, not bits of it.
And as Francesca and Planigale have pointed out, it's interesting that the Northern Isles have the most economic incentive of, perhaps, all of the UK to leave the EU, and a strong desire to remain part of the UK. If Scotland gains independence from the UK and remains within the EU, it might not be too long until the representative councils of Orkney and Shetland demand a local plebiscite on rejoining the UK and/or leaving the EU. Interestingly, Orkney and Shetland both fielded candidates for the 1987 UK parliamentary General Election who campaigned on a platform of the Northern Isles devolving from Scotland. They received significant levels of voting support (though a very long way from getting anywhere near winning), so in the current combustible,fractious and uncertain climate (and especially if Scotland became independent and an EU member), support might be an awful lot higher.
I'm finding it extremely illuminating that in every interview I've seen with Sturgeon (or "Nicola" if you're so inclined

) she's hammering home two points: 1) She and the Scottish Government will act "in the best interests of Scotland and the Scottish people", and (more importantly/interestingly) 2) If there is another referendum in Scotland, it will be focussed primarily on a "staying in" question, rather than a "leaving" question. In other words, Sturgeon is already seeking to frame any new Scottish referendum on explicitly and primarily gaining a mandate for Scotland to remain part of the EU, rather than explicitly seeking a mandate for Scotland to leave the UK.
This is an important (and pretty clever) repositioning/reframing by Sturgeon. Firstly, it at least partially deflates any argument (from the UK Government/parliament and any other stakeholders) that Scotland is seeking to have another "stay in UK vs leave the UK" referendum so soon after the first one; and secondly, if the result of such a referendum is a strong mandate for Scotland to remain within the EU, Sturgeon will use simple logic to infer that if a) the Scottish people want to remain within the EU, and b) the UK is in the process of leaving the EU, then the only way to implement the referendum outcome would be for Scotland to leave the UK.
In this way, Sturgeon and the SNP could almost get the Scottish independence they desire without ever having to ask that explicit question in any future referendum.
Of course, this strategy could be essentially scuppered if (for example) there's a November 2016 snap UK election which turns into a strange reassessment of the EU referendum result, and which results in the cessation of the "leave" wheels in motion and a repositioning of the UK within the EU.