An Unholy Marriage in Newton's Principia

Newton's masterpiece  Philosophiae Naturalis Principia Mathematica (or, "The Principia") stands as one of the most important scientific texts in history.   But modern people who read it have major problems with it (and not just because it is exceedingly thick and technical).  There are problems at one's gut level when it is examined.  Why? An odd marriage of faith and science within the same volume.  It was not odd for Newton's time, but is for ours.  He pairs theology along with the codification of the laws of motion, gravity, and geometric proofs.  An example of the theology from The Principia:

The Supreme God is a Being eternal, infinite, absolutely perfect; but a being, however perfect, without dominion, cannot be said to be Lord God; for we say, my God, your God, the God of Israel, the God of Gods, and Lord of Lords; but we do not say, my Eternal, your Eternal, the Eternal of Israel, the Eternal of Gods; we do not say, my Infinite, or my Perfect: these are titles which have no respect to servants. The word God' usually signifies Lord; but every lord is not a God. It is the dominion of a spiritual being which constitutes a God: a true, supreme, or imaginary dominion makes a true, supreme, or imaginary God. And from his true dominion it follows that the true God is a living, intelligent, and powerful Being; and, from his other perfections, that he is supreme, or most perfect. He is eternal and infinite, omnipotent and omniscient; that is, his duration reaches from eternity to eternity; his presence from infinity to infinity; he governs all things, and knows all things that are or can be done. He is not eternity and infinity, but eternal and infinite; he is not duration or space, but he endures and is present.

Our squirming has no end.  Many modern scientists squirm because their cart typically isn't attached to that horse.  What was the last issue of Nature or Scientific American to have theological contributions?  But many Christians squirm because their cart is attached to that horse, but a different breed.  Newton's public faith often deviated from traditional doctrine.    

The source (but unnecessary, I believe) of the unease is the separation of faith and science as disciplines.  Francis Schaeffer argues that humanity crossed "The Line of Despair" in the early 1900's where faith and reason were ultimately separated and people were forced to live either in the lower story of a house (reason) or the upper story (faith), but not both upstairs and downstairs within the post-modern framework.  Perhaps a lion's share of moderns' unease with The Principia, is that Newton lived on both stories of the house at once.  Or rather, he had no separate stories, just one unified abode where faith and reason lived together, shared meals, and (probably) argued about whether the toilet paper roll should pull up or down. 

In his book Orthodoxy, GK Chesterton describes the terrible result of the effort to separation faith from reason:

With a long and sustained tug we have attempted to pull the mitre off pontifical man; and his head has come off with it.