The Talmud as translated by Soncino in Brachot page 58 states:
Our Rabbis taught: On seeing the houses of Israel, when inhabited one says: Blessed be He who
sets the boundary of the widow; when uninhabited, Blessed be the judge of truth. On seeing the
houses of heathens, when inhabited, one says: The L-rd will pluck up the house of the proud; when
uninhabited he says: O L-rd, thou G-d, to whom vengeance belongeth, thou G-d, to whom
vengeance belongeth, shine forth.
One would have to clarify with their individual rabbis, if one or both of the underlined passages would be applicable to the destruction of the El Aksa mosque, and if so, does this apply only when there is strong reason to believe that the mosque will be permanently removed, or maybe even a temporary removal will require some type of blessing or prayer.
I myself, have not heard so far, a clear answer.