Muslims started the war back in March 1992 by launching a terrorist attack on a Serb wedding procession in front of the Serbian church in downtown Sarajevo, killing one member of the party and wounding several others. Interestingly, the fact that only the parishioners were violated, and not the actual physical church itself was actually hailed by the Muslims' supporters (the UN and false human rights groups)as a point in their favour. What else would you expect from atheist supporters of terrorists?
The barbaric assault in Sarajevo was immediately followed by Muslim and Croat attacks on not only federal (Yugoslav) institutions but any and all Serbian property, chief among which were attacks on Serbian churches and cemetaries. Among the first of many Serbian Churches to be destroyed in Bosnia was the main church in the city of Mostar, which was all part of the pogrom against Serbs in that city.
After that, all bets on Serbs not taking revenge against Muslim and Catholic houses of worship went to hell. The only people who expect Serbs to conduct a politically correct model of warfare which has never existed in human history are their enemies who delight in raising their "human rights" bar, as at Rambouillet, to a point which nobody on this planet can see.
It's necessary to recognize that Muslims have been destroying churches since the late 15th century when the Ottoman Turks (who were hardly devout in their version of Islam) conquered the Balkans. More out of spite than anything else, the Turks razed churches to the ground, and then used the foundation and much of the rubble to construct mosques which at first nobody, not even the Turks themselves, used for worship. This Turkish policy of constructing mosques on the ruins of Serbian churches was confirmed as recently as a few days ago in eastern Bosnia, when archaeological teams in Bijeljina discovered the original foundation of another 14th century Serbian church under the ruins of a mosque destroyed during the war in 1993.
The Serbian church was destroyed in 1530.
The same thing happened to thousands of other Serbian churches from the time of the original Islamic invasion right up to WWII and the present day. During the period under communism, the Croat dictator Josip Broz (known by the terrorist handle "Tito") not only prevented the reconstruction of Serbian churches, but actually allowed Muslims to build mosques on the ruins.
Many of the desecrated Serbian churches in throughout Yugoslavia, but especially Bosnia, Croatia, and Serbia's southern province of Kosovo, have been destroyed not once, but as many as three or four times. That is, of the small percentage of churches that have been reconstructed.
It's fascinating to watch the US and western Europe support the Balkan Muslims and the Catholic Croats carry out their campaign of destroying ancient edifices; frescoes and libraries, while actually claiming to uphold the values of western civilization. Sure, if your idea of western civilization is opening up a Burger King at a military base sitting on stolen Serbian land, then they are doing a terrific job.
Well, here's my two cents. I can only speak for Croatia, as that's all I've seen. What I saw were some churches were damaged or destroyed during actual fighting when both sides were shelling each other. Some were wantonly damaged or destroyed just for, I don't know, spite? What makes people want to destroy a church or a mosque? I realise that religious symbols often act as substitutes for national symbols in the Balkans, and the idea was to destroy a national symbol, but still, it's beyond me. Then again, I'm a foreigner, so of course I don't get it.
Along the border areas (and also along former lines of confrontation such as the Glina-Petrinja road) churches were damaged and destroyed by shelling and gunfire. Judging from the visible damage to other buildings near the churches, it did not appear to me that the churches were singled out for destruction. Neither did it appear there was any effort to spare them. (There may have been such cases; I just didn't happen to see them.)
In some cases, churches were shelled by BOTH sides during heavy fighting, such as the Catholic Churches in Moscenica and Sunya. There were also some cases where churches were shelled by their "own side" if those churches were situated on the "other" side of the CFL during fighting, such as the Catholic Church in Bilje.
Likewise, bell towers were sometimes taken off to deny them to snipers. I've already told the story about how the Croats blew off the bell tower of that picturesque country Catholic Church in the CFL near Osijek to deny it to Serb snipers. The footage was shown over and over on CNN to show how how horrible the Serbs were. The Croatian Army guys who were present at the time and later told me about it thought CNN's "stupidity" was hilarious, but, hey, it worked for them! I doubt this was an isolated case in border areas or any area where serious fighting took place.
Many churches were destroyed, defaced, looted, etc., in the complete absence of any fighting. I won't bore everyone with all the destroyed and damaged churches I saw, but only give a few examples. In the autumn of 1991, a bunch of Serb paramilitaries blew up and (later?) mined the ruins of the Catholic Church in Topusko. So far as I could see, there was absolutely no military justification for doing so.
Mr. Akashi's successor, Mr. Minh, had a thing about destruction of religious buildings, and we were tasked to monitor them. "Oh, great" I thought, "I've got this huge area of humanitarian basket cases scattered all over it, and you want me to babysit churches when it's all I can do to try to save lives?" But I did stop by and inspect churches when it was convenient (meaning I had to pass right by them while on humanitarian missions). I didn't see a one which was not damaged or defaced to one extent or another in the aftermath of Op Storm, some more than others. Perhaps Mr. Minh's directive helped somewhat, though, as predations on the Orthodox Churches abated some time after he issued it.
Particularly sad to me was the 18th century wooden Orthodox Church which was burned to the ground after Storm. It was in an extremely isolated area not too far from Glina. According to a book on history and culture loaned to me by a Croat intellectual, this church was a unique example of that particular period and style of architecture and had been amazingly preserved through the centuries. All I got to see of it was ashes. The Croats claimed 5th Corps (Muslims) burned it down, and I wouldn't be surprised at 5th Corps doing such a thing, but there was no evidence that 5th Corps ever entered that area. I can't say for sure who did it, just leave it as a question mark.
Anyway, all I know is that some folks in the Balkans have a thing for destroying each others' religious monuments, and it's been that way for a long, long time. Sad, but true.
There also seems to be a thing for desecrating grave yards. I saw little desecration of Catholic cemeteries, although they did fall into serious neglect in the Sectors during the RSK years. But there was not a single Orthodox cemetery left untouched in Sector North after Op Storm. The Croats managed to get them all, some being more damaged than others.