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But you see, when the sun comes out, ie, the light of empirical understanding, it pierces the fog revealing no object of worship at all, reminding us that throwing up our hands in the face of things we don’t presently understand and crying, “God did it!” leads to gods of gaps and the early truncation of inquiries that might have actually led to something worthwhile.

You're confusing natural theology with worship. The latter relies on resources beyond mere reason and observation, such as one's moral imagination and capacity for faith; the former does not. The fact that a scientist infers an intelligent designer or intelligent orderer from his reason and observation does not imply said scientist has truncated inquiry--- just the opposite.

For instance, Einstein inferred an ordering intelligence from the elegance of the physical laws he knew of, and based upon that conclusion inferred new laws that turned out to in fact reflect the way the universe actually is. In other words, one doesn't have to be religious to agree with Lewis or Gilder on this count. Einstein was no more religious than his hero, Spinoza, but both made the quite reasonable inference that a rational order, i.e. a logos, existed in nature.

The same inference was made by Locke, Newton, Galileo and continues to be made today--- in fact, the most prominent historical opponents of said inference, Hume and Kant, both praised it for its beneficial effect upon science throughout history, much as Charles Murray has today. Even Darwin did not take issue with the idea of an inference to such an intelligence--- he merely disagreed with the notion that such an intelligence must be moral. The theory that said inference promotes a woolly-eyed "god of the gaps" response is undermined by the actual empirical research of Charles Murray, not to mention the writings of Kant and Hume, who wrote with remarkable intellectual integrity in praising the historical benefits of an inference they themselves disagreed with.