Flickr/still wanderer.Last week the International Criminal Tribunal for the former Yugoslavia (ICTY) in The Hague overturned one of its most controversial verdicts. Last year’s convictions of Ante Gotovina and Mladen Markac, two of Croatia’s top generals, on war crimes charges were thrown out on appeal and within hours the men – who had been sentenced to 24 and 18 years respectively – returned home to jubilant crowds. For many Croats, this was cause for celebration, even euphoria, as the generals had been a stand-in for the country and its independence war two decades ago, which the ICTY had tarred with war crimes at a high level.

The joined cases had always been controversial, not least because they are wrapped up in Operation Storm, Croatia’s victory offensive in August 1995 which retook the nearly one-third of the country that had been under de facto Serb occupation since 1991. Storm, the largest military operation in Europe since 1945, involved 150,000 Croatian troops, who in only four days of fast fighting crushed the pseudostate called the Republic of Serb Krajina, which had been backed by Belgrade. Battle casualties on both sides were low, but there were isolated cases of murder, yet most significantly some 200,000 Serb civilians fled before the victorious Croats, making this the most successful example of “ethnic cleansing” in all the Balkan wars of the 1990s. Slobodan Milosevic’s dream of Greater Serbia, which caused so much unpleasantness in the Balkans twenty years ago, ended abruptly with the Croatian victory.

Croatia celebrates Storm every year on August 5as a national holiday commemorating those who died in the 1991-1995 struggle for the country’s independence, which they call the Homeland War. Croats point out accurately that Storm merely retook what Serb aggression, backed by Belgrade, had taken in 1991, and that tens of thousands of Croatian civilians were expelled from their homes early in the war from the Krajina region. Moreover, Zagreb always maintained that there was no plan to expel the Serbs, that it was a byproduct of Storm’s rapid success.

There was the rub. The ICTY took aim at Gotovina, a charismatic former French Legionnaire, because he commanded forces in the critical Dalmatian sector during Storm, while Markac led the paramilitary Special Police, which Serbs fingered with atrocities. Yet it was difficult to prove any high command responsibility for war crimes, not least because Croatia’s president and defense minister at the time, Franjo Tudjman and Gojko Susak, died in the late 1990s. The ICTY asserted that Gotovina and Markac had been part of a “joint criminal enterprise” that was collectively responsible for war crimes. Needless to say, this legal logic, which is inspired by American RICO statutes, was viewed as absurd in Zagreb, while many Croats felt it represented nothing less than the criminalization of the legitimate and defensive Homeland War.

Hence the celebrations across Croatia surrounding last week’s appeals verdict. Archbishop Josip Bozanic, the primate of the overwhelmingly Catholic country, hailed “the triumph of Truth,” while veterans went into the streets to celebrate, since the conviction of Gotovina in particular had seemed to put the whole country in the dock. Unsurprisingly, the new verdict has been greeted with anger by Serbs, who have always viewed the ICTY as a political more than a legal body, which has been more interested in Serb crimes than anyone else’s.

Belgrade is correct to view this development as a defeat for Serbia, since the Gotovina and Markac convictions had been a stand-in for the late President Tudjman, whom Serbs had professed was every bit as corrupt and nasty as the late President Milosevic – a viewpoint which last year’s convictions seemed to ratify. Yet that has now been overturned, and the indirect relegitimization of Tudjman and Homeland War has important political implications for the Balkans. At a minimum, Croatia, which has been a NATO member since 2009, can enter the EU next spring, on schedule, with its legal slate clear.

What has happened ought to raise questions about the efficacy of the ICTY, which is slated to shut its doors at the end of 2014 after two decades of trying to administer justice for Southeastern Europe, with uneven results. It now seems obvious that the Balkan tragedies of the 1990s would have been better served by a South African-style Truth and Reconciliation model, rather than the Nuremberg-lite ICTY, which has failed to bring healing to a region where it is very much needed.

NATO militaries ought to pay close attention to what the ICTY has done, not least because the logic of “joint criminal enterprise” – where generals can be charged with war crimes they had nothing to do with directly and may not even have been aware of at the time – has startling implications for any war where atrocities occur: which is to say all of them. Were similar logic to be applied to Iraq and Afghanistan, David Petraeus and John Allen would have a lot more to worry about than a tawdry sex scandal.

John R. Schindler is professor of national security affairs at the Naval War College in Newport, RI, and a former National Security Agency official. The views expressed here are entirely his own.