This is a reasonable argument, except it doesn't seem to reflect what you wrote in your original criticism!

To my mind, you had two big thrusts of complaint against scientists.

The first was perhaps most succinctly phrased by you as, "Thus, the scientist doesn’t refute animism so much as ignore the universe’s apparent or at least possible vitality."

With terms defined as such: "The animist perceives natural activity as resulting from underlying mental causes or at least she presumes as much in her respectful or resentful handling of natural processes. But the scientist posits only the likes of energy, force, inertia, and godless natural law."

But the latter claim is just completely wrong. We have astoundingly good models of many physical properties that don't admit any room for "mental causes", unless the mental agent has a perplexing fetish for calculus and a complete lack of any imagination. Once we start trying to apply the same principles--identification of fundamental forces, for instance--to things that actually are mental in nature, e.g. human psychology, we get failures so spectacular that we don't even talk about them as serious ideas any longer. The idea that scientists ignore the universe's vitality is just completely contrary to how research actually works. Scientists repeatedly ask, "Hey, how can we explain this?" For physical phenomena like turbulence, even though it's extremely complicated mathematically, and (mathematically) chaotic so long-term prediction is impossible, there is no evidence of anything extra. In other cases--where the subject is alive, and with mental capacity--of course, that is taken into account. That you don't need to impute mental states to, say, weather is a result not an assumption.

The second part of your thesis seems to be, "Here we see that scientists and modern folk generally have an antisocial relationship with the world."

I take particular objection to your use of the word antisocial as opposed to asocial, because anti implies that it is actually hostile to what is social, rather than simply being irrelevant. But this is what I addressed before: in those cases where a more humane, compassionate perspective is necessary, these days as opposed to half a century or a century ago, is mostly being led by scientists. The implication is very strong--even if you don't quite state it, that "We objectify nature with artificial, unintuitive descriptions and pragmatic models, and with egoistic cultures that rationalize all manner of human brutality." is the fault of science and scientists.

The problem is, it's not. Having distinguished between poorly-predictive superstition that might leverage well our impressive capabilities for interpreting the motives of other intentional beings, and how things actually work, scientists have not just decided, oh, well, who cares, let's brutalize everything.

Quite the opposite: they tend to recognize what is remarkable and fragile, what is wonderful and inspiring, in addition to what is useful and how things work. You don't have to be an anamist to think that humans, at least, can value things, and to abstract this into a more general notion of this-has-value. The scientific argument is mostly, these days, to not brutalize things, because the things are wonderful, because some of them have feelings (and our empathy extends that far), because there really actually fundamentally aren't huge differences between people, and so on. Except instead of our sympathies being based on falsehood--flat-out 100% genuine wrongness--they're based on how things are, and human sentiments about what is valuable.

So, yes, there do seem to be some "brute primitives" that need to be accepted to make sense of the universe. (That we use the term "brute" with all its unpleasant connotations speaks more to the lack of charity of those who coined and used the term, though, than the state of affairs. Why "brute" not "resplendent" or "facilitating" or any other word?) But the linguistic suggestion that a "brute primitive" gives rise to an attitude of "construing nature as worthy of being only enslaved" is completely wrong. Use of flowery language is not an argument, even if it is effective at manipulating the emotions of the listener into being predisposed to accepting a particular point of view. (Likewise with "zombification"--zombies are not merely mindless, they are also disgusting and scary and we are well-advised to destroy them. The technical point might be true, but the connotations are BS when taken to be a scientifically-informed perspective.)

It is historically accurate that arguments for withholding compassion were widely made by referencing the mechanistic nature of the universe--that's at least as old as Descartes. But we're not arguing with Descartes any longer.

The actual state of affairs now--which you haven't offered any evidence against, by the way!--seems to me to be that scientists more than any other segment of society are leading the charge against the brutalization of nature. And the reason is that we understood, and realized that many things that we have are precious, if anything is to be said to be precious at all.