Nationalism and Catholicism

See here Cranmer has a post on his blog today about the Pope's visit to Croatia and his urging of that country to join the EU despite fierce opposition around the loss of national identity. Read the post for a well informed analysis.
My issue is about some points raised in the post about Croatian Catholicism and Croatian  nationalism, if it is possible to seperate the two in practice. Given the history of Croatia during World War 2 and the more recent events in the wars in Yugoslavia in the eigthies and the atrocious ways in which "fervent" Catholics treated their enemies, armed and unarmed, the question arises about the nature and the influence of Croatian Catholicism. Going back even farther to World War 1, we have the Vatican encouraging the "Catholic Austro-Hungarian Empire in attacks on Orthodox Serbia, leading to religious and ethnic cleansing and, of course, the Great War itself. The kind of nationalism that has bedevilled(interesting word) the Balkans is extreme and dangerous. It is easy to absorb a religious faith into it, particularly when your enemies have a different faith as the Orthodox Serbs have. But in conflating the two, inevitably the nationalism proves stronger and re-defines the faith to support its pupose. Catholicism or Orthodoxy should never be so strongly identified with any nation. Faith and religion transcend national boundaries, they are universal. If we forget that we find ourselves needing to paraphrase Mme. Roland facing execution in revolutionary Paris:"O religion, what crimes are committed in thy name."


So,for the Vatican is it not only a question of my country right or wrong but also Catholic right or wrong? And is the Pope now  running the risk of identifying with and seeming to support some very unhealthy and un-Christian understanding of what Catholic means.
The Pope will pray at the tomb of "Blessed" Archbishop Stepinac, who was created Blessed by Pope John Paul 11 after his persecution and suffering during the post-war Communist regime in Yugoslavia. There remain however great uncertainties about his role during World War 2 and his links to and support of the facist Ustashe who undoubtedly were every bit as bad as the Nazis in their persecutory zeal.
A difficult visit then and one that might have been better avoided. They say never talk about politics and religion. The Vatican needs to get better at seperating the two.