Why Would Those Dastardly Israelis Bomb Mosques?

Mosques, like churches are places of worship. They should be considered sanctuaries. Well, not exactly. As the Ayatollah Ruhollah Khomeini wrote in his study Islamic Government (bolding mine):

Do not allow the true nature of Islam to remain hidden, or people will imagine that Islam is like Christianity (nominal, not true Christianity), a collection of injunctions pertaining to man’s relation to God, and the mosque will be equated with the church. . . .

The Commander of the Faithful [in the seventh century A.D.] was also a ruler; he ruled over all the Muslims and the whole of the broad Islamic realm. Were you more zealous than he in promoting the glory of Islam, the Muslims, and the lands of Islam! Was your realm more extensive than his! The country over which you ruled was but a part of his realm; Iraq, Egypt, and the Hijaz all belonged to his realm, as well as Iran. Despite this, his seat of command was the mosque: the bench of the judge was situated in one corner of the mosque, while in another, the army would prepare to set out for battle. That army was composed of people who offered their prayers regularly, were firm believers in Islam; you know well how swiftly it advanced and what results it obtained!

You cannot equate the nature of the church in Christianity to the mosque in Islam. It's apples and oranges, as you can see in the following IDF video.