The way that most civilized nations have multiple peoples living under the same nation is a clear seperation of church and state. What Muslim is going to live under Jewish rule? What Jew is going to live under Muslim rule? Or even if the split the land down the middle and run each side independently, there is still the threat of conflict.
Theoretically they should be able to live under one nation as long as the state passes no laws that prohibit religious freedom. Works for the rest of the world.