... but the EU isn't just a free trade organisation anymore? It has a common agricultural policy, common foreign policy and what next over the next 20-30 years? a common energy policy?
Yes, it does other things and some of those things are sensibly centralised. Some are a complete mess for reasons largely unrelated to their centralisation (e.g. the CAP and CFP) while others are less a matter of centralisation and more a matter of having more heft as a co-operative group of countries than as individual nations (e.g. the vestigial foreign policy).
Eventually, the EU may end up as a federalised state, but that's not what the EU referendum will be on.