Your criticisms are thought-provoking, as always. I'd rather not get tied up in a sprawling debate, though, at the moment, because these are pretty big issues that can be taken in different directions, and I'd rather be writing articles.
I'll just say that I agree that nature might evolve morality or social instincts to make us feel better about our lack of centrality to the universe. The question is whether we're puppets of nature or whether intelligence can backfire, enabling us to see through the evolutionary roles and to question the functional meaning of life that the genes evolve.
I agree also that "nature's indifference" might imply theism, strictly speaking. The root of the problem isn't nature's lack of concern one way or the other, but its inhumanity or monstrous, amoral, godless self-directedness.
I say in the article that there are likely different senses of "creativity" at play, so I agree there's the potential for equivocation. But I don't see how you can read modern cosmology without noticing a supreme degree of self-creativity at work in the universe. We can call this "evolution," "development," or "emergence" instead, but the point is that the complex natural order emerges from much simpler states, according to science.
I'm not specifying the aesthetic judgments to apply to nature, so I'm not saying "beautiful" suffices as a way of honouring universal creativity. These are separate questions: Are some aesthetic values universal and objective? What's the most fitting aesthetic judgment of nature? We might lean towards a negative assessment, along Schopenhauer's lines.