Ed, No the Gedolim do not call for Hafganos in Yerushalayim for rock throwing violence. These acts are few in numbers (yet blown out of proportion by the zionist/secular media who attempt to make it appear it is widespread), committed by bored youths who have no shaichos to Gedolei Yisroel Shlita.
What Gedolei Yisroel Shlita DO call for, are rallies to protect Kovod Shabbos Kodesh.