I don't consider this to be vastly important, in the long run. The EU states don't have much force projection military power, or the will to use it. I don't think the Lisbon treaty portends much for AI, really. The nations within (and subsets of the whole) still have their own agendas.

Crucially, the EU still doesn't really have sovereignty over "EU territory". They won't have sovereignty until they have a coherent centralized military capable of controlling every EU nation-state. This is unlikely to happen in the next 50 years. If a member state wanted to leave, they could.