It might be terrible, but there is no way around it as it stands. A European superstate might be realised in the (very) distant future, but until that members will keep leaving/joining, whether we like it or not. With that in mind, and the fact that attitudes and opinions do change from generation to generation, I believe that well-regulated referendums are the way to go. And with well-regulated I don't mean individual members holding a referendum on a whim, but a general rule that, say after 20 or 25 years (a generation), the member states
should sort out if the union is still for them. We would move away from the dream of the EU as a self-fulfilling prophecy, to a true union of economy AND values that the current people living here agree to.
Needless to say we would need certain automatisms in place when members leave, some sort of basic blue print how to treat an exit (as opposed to the chaos we have now), but that should be doable. Maybe the Brexit will even be that blue print.
Holding a referendum in all countries at the same time could be an idea, as I said in 20-25 year gaps. Long enough to plan, short enough to pull out if a member realises that pulling out might be the better idea.
And as for parties using referendums to pressure other members, that will always happen no matter what. Even on a state level, as we can see with Catalonia. But I see nothing wrong with the EU facelifting itself from generation to generation.
The ambiguity is intentional, interpret it as you will!
Point I was trying to make, without projecting anything, is that everyone (should) understand the basic path to making an educated decision on a big topic. If people spend hours upon hours arguing about the acquisition of a car, they should put at least this much effort on -exit referendums. And even if they don't, splitting the Brexit in 2 referendums would have at least forced them to think twice, with more information on their hands.