The root of the matter is the long years of exile and suffering that the Jews underwent at the hands of non-Jews. Those years gave birth to extensive halakhic and kabbalist writings. Central portions of those writings turned the pain into secret vengeance that could not be actualized. Protected by their inability to take practical action for revenge, the great rabbis of Israel let loose with detailed descriptions of the inferiority of the "goyim" (non-Jews), the vengeance they deserve and what would be done both to them and to Jews who collaborate with them after the Messiah's arrival.What sick bastards most of them are!
Even the humanist rabbis of our time have not apprehended the intensity of the Zionist revolution, the immigration to the Land and the transition from an era of exile to an era of redemption. Suddenly, in Israel, everything becomes practical, certainly in the eyes of those who view our time as the start of the time of messianic redemption. Suddenly, everything written as a powerless victim's cry of pain can, and indeed is, turned into instructions for violent action.
The point is that without dealing with the halakhic and ideological roots of the problem, there is no chance for those who want a different Judaism. Good intentions will not suffice. Intellectual courage is required. The halakhic-Orthodox path is open and waiting. The Gemara in Pesachim 34 quotes Rabbi Yirmiya as making a statement that deals vigorously with large parts of the tradition. Rabbi Yirmiya challenged the wise men of Babylon: "You sit in a dark land, speaking words of darkness." In other words, those interested in freeing Judaism from the messianic-racist-vengeful world that has swallowed nearly all of it can do so only if they dare to stand up to the canon and remove the racist, the violent and the vengeful from it - even if, indeed especially, if it was written by the greats, like the Rambam, Ramban, Ramhal, Yehuda Halevy, Hazohar Hakadosh and the Ari.