answer the question: did carbon exist in the world when God looked at all that He had created and said it was "very good" ?
Isaiah 45:7
"I form the light, and create darkness: I make peace, and create evil: I the LORD do all these things"
Not that Carbon is evil in of itself, but rather how it is used I suppose.
or did He originally create everything with a silicon-based chemistry?
Now that is another subject entirely.
Sand of the Sea is Silicon...
Revelation 13:1
"And I stood upon the sand of the sea, and saw a beast rise up out of the sea, having seven heads and ten horns, and upon his horns ten crowns, and upon his heads the name of blasphemy"