Well, NJ, perhaps then we should just stick to the "Swiss model" of requiring a majority of regions in support of the measure. Otherwise you could have, say, a referendum passed because London, Leeds, Birmingham and Manchester were in favour but nowhere else was, and still passing, which could indeed amount to "tyranny of the majority".
I think before the EU referendum there was talk, mainly from the SNP, that it should be a rule that *all* of the nations of the UK should be in favour to require the EU referendum to pass. That, at least, was a fairly transparent excuse to stop it from passing altogether, but at the very least illustrates that regional divides do exist and shouldn't be trampled over. I think my "majority regional" rule would probably have seen the EU referendum pass, because it seems to me to make no sense to count all of England as just one region. I'd probably have picked either counties or constituencies, and, as far as I remember, a majority of constituencies also were in favour of leaving:
https://docs.google.com/spreadsheets/d/1wTK5dV2_YjCMsUYlwg0l48uWWf44sKgG8uFVMv5OWlA/edit#gid=893960794
So long as the principle behind drawing up referendum rules isn't that you pick rules deliberately to block results you don't want to happen, then I hope it's still clear that there's a case to be made for enshrining the rules we do have about conducting referendums in law properly, once and for all.