Whatever the Israeli government would have done, the destruction of the shuls was a forgone conclusion after the disengagement. No one really believed that the Palestinians would prevent the buildings from being destroyed. I agree with what Israel did for the following reasons:
1. Most of the poskim who were asked (including R' Ovadya Yosef and other prominent poskim) agreed that it was prohibited for Jews to destroy the shuls
2. It would set a bad precedent worldwide
3. The Palestinians got bad PR from the destruction
I am sure that many people when hearing/seeing the destruction thought what barbarians, we would never do that to a mosque. While it is true that the Israeli government (or the US government) would never do that, the halacha may require us to do just that. The Torah commands us to destroy Avoda Zara especially in EY, so if Islam is considered avoda zara then mosques would need to be destroyed. Even if it is not avoda zara, a mosque certainly has no kedusha and is no different then any other building.
Again, we see the conflict between the Torah and Western values. There is an international treaty prohibiting the destruction of any religious site, while the Torah commands us to destroy avoda zara.
In fact, the parshiyos that we have read lately and are reading in Devarim, are very un-pc. In parshas Reah we have the din of עיר הנדחת, where if the majority of people worship avoda zara we raze the city and kill ALL the inhabitants, in Shoftim we have the halachos of war, including the halacha to wipe out the 7 nations. In this weeks parsha, Ki Tetze, we have the mitzva of wiping out Amalek.
On Rosh Hashana, we emphasize the Akeda. If we think about it Avraham Avinu was willing to kill/sacrifice his son to fulfill the will of Hashem. Again, this is something that conflicts with the Western sense of morality. Avraham Avinu who was the איש חסד par excellance was able to overcome his feelings of חסד and fulfill the will of Hashem. Not only that, this act did not affect him negatively and he remained the איש חסד par excellance. In passing the test of the Akeda, Avraham Avinu passed down to us this quality, that we have the ability to fulfill the will of Hashem even where it is seemingly cruel and not be affected by it.
I am not advocating actually doing any of these things today, we cannot. My point is that we need to look at the halachos relating to these issues and from there understand the Torah's idea of morality/justice and how it conflicts with Western morality.