Israel having only one religion is not a problem, because they're also the only Jewish nation. For example, if you have each religion contribute one improvement, you can have Judaism contribute two. Wonders are different. Only one wonder or so is needed for Judaism, because a wonder which requires Judaism will go to Israel without contest. (Obviously, it should be the Temple Mount, or Solomon's Temple. I'm not sure what name to go with, but it's pretty clear-cut.) If another civ had Judaism plus another religion, it would be hard to balance, but with only one civ having Judaism, there should be no problem. Judaism can simply function as both religions for Israel.