The way I see it, Ghostmaker, is that the EU infrastructure goes a long way in preventing sectarian nastiness and nationalist tendencies from influencing public policy. Things like protectionism, regional disputes, etc. are ever so much easier to resolve in the context of the EU superstructure. Furthermore, the EU helps to incalculate identities that go beyond national units. That, in addition to the economic and political ties, is precisely WHY war is unthinkable and laughable now.
Sure, the EU is wasteful in a lot of ways. But when it comes to a lot of European co-operation, a body that regulates and provides an effective and accountable conduit to that co-operation is much better than individual states hashing it out on thier own.
Remember always that the probable alternative to the EU is not some peaceful, happy, secure, sectarian-free, free market enterprise paradise. If that were the case, I'd say 'hell, scrap it all!'. But it just isn't, unfortunately. At least not yet.