While I understand where you're coming from with the idea of "over-representation", I diverge with you after that point for several reasons. First, to say that Israel is not an historical or political force in the world, let alone that region, is debatable to say the least. For a period of several hundred years during the time of the second temple, the religion of the Israelites was something of a spiritual world wonder, marveled at in the form of Herod's temple by the known world, including pagan civilizations. To say that Israel belongs in a game like RFC is anachronistic. Israel was never an empire per se. To include it in RFC RAND, to me, is almost necessary. RFC RAND is very much about alternate histories and seems a perfect stage for Israel to make its debut. Second, to say that "Judaism" is an appropriate representation of the Hebrew people is a bit off the mark. The cult of Yaweh was a lot of things before it was Judaism. I'm assuming you're mostly referring to the Diaspora phenomenon, but even then, Jews and their ancestors have a history that extends back far past that, to a homeland they inhabited for quite a long time. Third, your representation comment. Two things on that. The Middle East is no more a "region" than Europe is, and look how over-represented European civs are. Secondly, there certainly is an abundance of Islamic-influenced civs (And yes, early Semitic, Persian Turkish etc), and I don't think that's wrong. What I take exception to is that they somehow adequately represent the profound impact that the civilization, religion and concept of Israel have had and still have on our world.
In summary, for RFC Yerushalayim and Solomon's Temple stuck in it is fine. The original RFC actually overrepresented the religion and would have been better off including it as more of a cultural mechanic. To not be able to play as this civilization in what amounts to an alternate history mod, however, is a damn shame.