I will start with this caveat: I did not read the entire article before posting, but pretty much just the first page.
Of course, the reason Judaism is important is because it was basically the first major religion to be monotheistic (hence its foundation with monotheism). They were spread widely (though generally not the dominant force) across the classical world. Kazakstan was once a Jewish Empire in the medieval period as well.
However, for game purpose, I would go with Zoroastrianism (perhaps with priesthood?).
The main reason, if you start splitting up Christianity, how will the factions feel about other factions? I mean, Protestants and Catholics went to war, for example, but most agreed that Islam was a bigger threat. Also, what about splitting up other major faiths, sunni and shia, etc? Leave major religions intact.
However, all this being said, I don't think that Judaism should be taken out...