If God Is Dead...

... then as Will WIlkinson explains none of the things Ramesh Ponnuru is worried about here actually follow. As Will says:

Suppose you know that there is free will or that moral reasoning is not futile. Next, suppose you find that the universe is made out of only whatever the universe is made out of. What do you infer? You infer that free will and moral reasoning, which occur inside the universe (or as aspects of the universe), whatever they may be, are made possible because of whatever it is the universe is made out of. And there you are.

David Chalmers tackles some related issues in his relatively accessible paper "The Matrix as Metaphysics". One point to note is that even within the materialist framework we've experienced some rather stunning revelations as to what the world is made of. The discovery, for example, that matter is composed of atoms didn't lead everyone to freak out and say "oh my God! I used to think the kitchen was full of cookware but now I know it's really full of atoms!" Rather, the kitchen continues to be full of cookware, but the cookware is made of atoms.

Then you learn that the atoms are made of subatomic particles. That, in fact, the atoms are mostly empty space. That the subatomic particles obey the odd principles of quantum mechanics. All kinds of weird stuff. None of this, however, undermines your pre-existing knowledge of the macroscopic world. Pots hold water, but colanders don't. It's interesting to learn more about the ultimate nature of matter, but that doesn't make our everyday knowledge of the world endlessly renegotiable. Similarly, moral reasoning does in fact make sense -- people do it all the time.