I think it's another one of those cases where you also have to ask yourself whether it was primarily a religious affair or rabid, secular-minded nationalism attempting to eke out some credibility for itself by claiming to be motivated by religious principles.
It's another example of where Roman Catholics are faulted for failure to condemn and oppose, but... they kind of did. Archbishop Stepinac was one of the first outspoken critics of the new Croatian regime, much the same way Bishop von Galen in Germany was one of the first (if not the first) critics of the Nazis' racial theories from a Christian theological perspective.
Stepinac in particular said in 1942: "We categorically affirm that all peoples and races on the face of the earth have the right to life and to treatment consequent with their dignity as human beings." Meanwhile, "Friar Satan" Filipović was formally expelled from the Franciscan order in 1942, though he still portrayed himself as a monk and the state was happy to continue to purport him as such so long as it suited their purposes.
If the perpetrators of these crimes had actually cared about religion, they would have listened to their archbishop and removed Filipović from his post.
