Spain wants Gibraltar(sp) back now too.
They've wanted Gibraltar back from the moment they lost it. They're still not going to get it. Gibraltarians, unlike Scots, actually like being British, and if the Brits'll travel halfway around the goddamned globe to defend some sheep-fuckers in the Malvinas, a little economic setback from leaving the EU ain't gonna stop 'em from defending their own backyard.
It's more complicated this time around. Gibraltar voted overwhelmingly for Remain. They don't want to return to the pre-EU days of having to cross a real international border just to leave work.
They don't want Spanish jurisdiction either. But they might go for it if it meant EU access. Or they might not; hard to say really, they really don't want to be Spanish.
The Civil War set the precedent, and we have the amendment that States can not leave, but at the time it wasn't as "set in stone".
I'm not saying the Civil War didn't set a precedent, but I'm not sure it was a legal one. To my knowledge there's no actual constitutional bar on secession, just the history of armed response and the opinions of various jurists who have been asked the question now and then. Of course, people may question the legality, but I don't think anyone questions the idea it'd receive a chilly welcome.
The rest of your post made some good points, though.
There are quite a few precedents on accession to the United States, and a constitutional method outlined for how new states get admitted. States could also be allowed to leave via the same mechanism. It's just that none ever have.