Part and parcel of Nietzsche's claim that God is terrified of science, is his intense hatred for Christianity. His hatred of Christianity is not some pathological or illogical product of childhood trauma or some psychological disturbance related to Christianity; it's based on the point this thread would like to point out, and which Nietzsche's great philosophical mind intuited immediately based on the correctness of so much of his other ideas: Christianity is a great and grave threat to throw a wrench into the metaphysical balance based on an eternal binary relationship between Yin and Yang; a balance/relationship that since its eternal, can never be overcome.
Nietzsche intuits that whereas all other human thought (religious or otherwise) has a built in genuflection to binary-objectivity (an objectivity thought to empower science over theology), Christianity thumbs its nose at this quasi-universal binary-objectivity. Which is to say that whereas human thought generally recognizes the fact that there are always two poles, opinions, or ways to interpret a matter, such that dogmatism is misplaced in dialogue, Christianity threatens to upend that apple-cart in a manner that Nietzsche better than most understands.
I regard Christianity as the most fatal and seductive lie that has ever yet existed — as the greatest and most impious lie: I can discern the last sprouts and branches of its ideal beneath every form of disguise, I decline to enter into any compromise or false position in reference to it — I urge people to declare open war with it.
Nietzsche, Friedrich, Delphi Complete Works of Friedrich Nietzsche (Illustrated) (Series Five Book 24) (p. 3180). Delphi Classics. Kindle Edition.
Though many people agree with Nietzsche's statement, few fully understand either the vehemence, nor the genesis and power of the statement. Nietzsche singles out Christianity and Christians as something like the fly in humanity's ointment so far as the true, eternal, purpose and reality of the world is concerned. For him, Christianity is far from a garden variety menace to society and reality.
On the contrary, Nietzsche realizes how deep Christianity has wedged its pry-bar into the very axis of eternal balance. Christianity threatens to pull back the curtain on the metaphysics of unbelief that every creature from the hand of God once assumed (and still does for the most part) would allow for the fact that unbelief could never be treated as anything other than, at worst, one pole in the Yin and Yang of reality; unbelief would be eternally free from answering to its disbelief.
Through the prism of his great genius, Nietzsche saw the truth of Christianity and was moved to immeasurable hatred, for fear that it would relieve him of the ace card he intended to play against the Living God: a belief that unbelief is metaphysically, eternally, part and parcel of a natural and good balance that's everlasting. Christianity threatens to undo the binary nature of truth and reality by destroying the eternal balance of Yin and Yang.
Upon this theological instinct I make war: I find the tracks of it everywhere. Whoever has theological blood in his veins is shifty and dishonorable in all things. The pathetic thing that grows out of this condition is called faith . . ..
Friedrich Nietzsche, The Anti-Christ (Kindle Locations 272-274). Kindle Edition.
John