I agree with your worries tbf. I just think something so deliberately polarising as a referendum, on something so fundamental to a country as how it functions legally, politically and economically, is always going to lead to the kind of ructions and ridiculousness that we have now. We're 6 months from leaving and it gets worse by the week.
I realise you're likely thinking of Scotland and that it would make independence that much harder, and it's an interesting case given the SNP are literally a party founded upon the idea and had won parliamentary elections multiple times before the vote. It's tough to strike a balance, but it just seems to me that the current way of doing it is insane

It would also doom any chances of electoral reform here, but let's be honest, that's not happening anyway.