The Protestant theologian Rudolf Otto wrote about the “mysterium tremendum et fascinans,” the nature of God as a “terrible and fascinating mystery.” One of his theories was that Islam was fundamentally a religion of the “mysterium tremendum,” de-emphasizing the compelling aspects of the divine to focus on its terrifying side. Whether or not this was a valid assessment is not for me to say, but it's definitely the feeling behind this song. The God they're talking about here- which may not be the same as the God the musicians personally believe in, if they believe in any- is the God that smites cities and turns people into pillars of salt, not the God of “love thy neighbor.”
It's not at all clear that this song is meant to be taken completely seriously, but it still communicates the terrible mystery for all that. Whatever your personal religious beliefs, the combination of Natacha Atlas's Arabic wailing with the dark lyrics and music of Juno Reactor is numinous indeed. For an amusingly different take on the same song, look up the cover version by Laibach.