Don’t get distracted, this back road is purely about having 2/3 majorities for things like referendums. If, for example, the Lisbon treaty had only gone 50/50 (yes, I’m aware there wasn’t a vote) then sure, it should have gone back to be reconsidered. Maybe that would result in stalemate, but what better incentive for the ‘unelected’ management to go back and do something the electorate wanted for a change?
Same with Brexit. If we had a higher bar to cross, perhaps the 50/50 vote would have brought about positive change, rather than the mess we have now.
Of course you could argue (and probably will) that it would simply give the EU the impetus to carry on regardless. I’m sure there’s some mechanism which can be devised to prevent that happening though.