I get the feeling from your posts that you do not accept scripture as authority for your theology. Thus, I see no use in discussing the theoloigcal ramifications of the article above. If you cannot accept the scripture as autoritative, then your theology is subject to every wind of doctrine.
In response to your post, who do you think created the universe? Who set into motion this First LAW of Thermodynamics? Is the First Law of Thermodynamics superior to God?
The Bible is quite clear on this. If there is a Law of Thermodynamics it is because GOD decreed that law at the creation. God works within the natural laws because he decreed those natural laws.
Col 1:16 for in him all things were created, in heaven and on earth, visible and invisible, whether thrones or dominions or principalities or authorities--all things were created through him and for him.
Col 1:17 He is before all things, and in him all things hold together.
Thus even the particles that make up the atmos in our universe are held together by the power of the Word of God.
If you wish to limit your God to a being who must work with existing materials to create, then you believe in a lesser God than the God revealed in the Bible.
You are free to worship such a being, but you must remember that if you are wrong about the nature of God you may be very well wrong about your status before him.
BTW if you get your theology from a Julie Andrews song, I can guarantee you that you are headed for Hell. :-)
But what if the materials did exist from all eternity?
Would God be guilty of "waste" if He were to create the universe out of new material when there were already perfectly good atoms, just waiting to be used?