Ha'aretz recently ran a piece about Israeli archaeology in the 1950s, when dozens of Mosques and holy places were razed to the ground. It's worth a read:
In July 1950, Majdal - today Ashkelon - was still a mixed town. About 3,000 Palestinians lived there in a closed, fenced-off ghetto, next to the recently arrived Jewish residents. Before the 1948 war, Majdal had been a commercial and administrative center with a population of 12,000. It also had religious importance: nearby, amid the ruins of ancient Ashkelon, stood Mash'had Nabi Hussein, an 11th-century structure where, according to tradition, the head of Hussein Bin Ali, the grandson of the Prophet Muhammad, was interred; his death in Karbala, Iraq, marked the onset of the rift between Shi'ites and Sunnis. Muslim pilgrims, both Shi'ite and Sunni, would visit the site. But after July 1950, there was nothing left for them to visit: that's when the Israel Defense Forces blew up Mash'had Nabi Hussein.
This was not the only Muslim holy place destroyed after Israel's War of Independence. According to a book by Dr. Meron Benvenisti, of the 160 mosques in the Palestinian villages incorporated into Israel under the armistice agreements, fewer than 40 are still standing. What is unusual about the case of Mash'had Nabi Hussein is that the demolition is documented, and direct responsibility was taken by none other than the GOC Southern Command at the time, an officer named Moshe Dayan. The documentation shows that the holy site was blown up deliberately, as part of a broader operation that included at least two additional mosques, one in Yavneh and the other in Ashdod.
David Eyal (formerly Trotner), who was the military commander of Majdal at the time, says "he does not want to return" to that period. The historian Mordechai Bar-On, who was Dayan's bureau chief during his term as chief of staff and remained close to him for years, says he himself did not serve in Southern Command at the time and therefore is not familiar with the destruction of mosques in Ashkelon, Yavneh and Ashdod, and also never heard Dayan issue any such order.
"As a company commander in Central Command, we expelled the Arabs from Zakariyya, but we did not destroy the mosque, and it is still there," Bar-On says. "I know that in the South, in the villages of Bureir and Huj [near today's Kibbutz Bror Hayil], the villages were leveled and the mosques disappeared with them, but I am not familiar with an order to demolish only mosques. It doesn't sound reasonable to me."
The affair of the mosque demolitions does not appear in Kletter's book "Just Past? The Making of Israeli Archaeology," published in Britain (Equinox Publishing) in 2005. Kletter, who has worked for the Antiquities Authority for the past 20 years, does not consider himself a "new historian" and has no accounts to settle with Zionism or the State of Israel. Nevertheless, the story of archaeology comes across in his book to no small degree as one of destruction: the utter destruction of towns and villages, the destruction of an entire culture - its present but also its past, from 3,000-year-old Hittite reliefs to synagogues in razed Arab quarters, from a rare Roman mausoleum (which was damaged but spared from destruction at the last minute) to fortresses that were blown up one after the other. Had it not been for a few fanatics like Yeivin, who pleaded to save these historical monuments, they might all have been wiped off the face of the earth.
As the documents quoted in the book show, only a small part of this devastation occurred in the heat of battle. The vast majority took place later, because the remnants of the Arab past were considered blots on the landscape and evoked facts everyone wanted to forget. "The ruins from the Arab villages and Arab neighborhoods, or the blocs of buildings that have stood empty since 1948, arouse harsh associations that cause considerable political damage," wrote A. Dotan, from the Information Department of the Foreign Ministry, in an August 1957 letter that is quoted in Kletter's book. A copy was sent to Yeivin in the Department of Antiquities. "In the past nine years, many ruins have been cleared ... However, those that remain now stand out even more prominently in sharp contrast to the new landscape. Accordingly, ruins that are irreparable or have no archaeological value should be cleared away." The letter, Dotan noted, was written "at the instruction of the foreign minister," Golda Meir.
The piece is long-ish, but well worth reading in full. It tells of a systematic destruction of Palestine's Arab past, including Israeli soldiers' raids into museums and archaeological digs in order to steal and destroy artifacts and burn down the offices of foreign archeological expeditions.