The rabbinical courts exist for sorting out religious issues, such as religious marriages and divorces of Jewish citizens. Judaism is not even special-cased: «Such courts exist for the recognized religious communities in Israel, including Muslim courts, Christian courts, and Jewish Rabbinical courts.» (Wikipedia).
The Basic Laws, which sort of comprise the makeshift constitution of Israel, don't seem to make any religious references, but rather refer to the founding UN principles like human rights.
you know such a clause in a rental agreement would be legal in the US as well, right? Binding arbitration clauses are legal in rental agreements at least in many parts of the US and agreeing to a rabbinical court to be the arbitrator is legal as well.
The Basic Laws, which sort of comprise the makeshift constitution of Israel, don't seem to make any religious references, but rather refer to the founding UN principles like human rights.