If you really want to get rid of ahistoric units, you need to replace Egypt entirely. At this point in history, Egypt was a successor kingdom like the Seleucid Empire.
Maybe you should consider trying Europa Barbarorum (or it's rival, Rome: Total Realism) for your next campaign? Both mods spice up the game, in addition to making it more accurate. I've only played EB, but I liked it very much. It's more complicated than vanilla R:TW, though.
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