Hmm, I think its a fair argument to make that countries being part of a cooperative union with mutual dependencies and closer relations has played a role in keeping peace in Europe, particularly amongst those with ambitions to join. That is not to say it is the only reason but it has certainly played its part.
I would agree it may have played a part in dissuading some of the smaller states (in the last 10 years) from making bigger issues of border and ethnic disputes whilst they await EU membership,but to be honest the major factor IMO was Nato demonstrating in the balkans that genocide in Europe again was not to be tolerated