Well, yes, because you haven't presented any evidence for hypocrisy. I also happen to be very familiar with the field, so yes, like most things with no evidence presented which is also strongly at odds with personal experience, I ignore this possibility. I ignore oodles of possibilities like this.

You also say about yourself that "I focus on the evident role played by scientific institutions in developed societies". But you don't tell us about this. Instead, you give characterizations that seem straight out of the age of industrialization, where everything was treated like a machine (very trendy, since we were just figuring out how to make complex machines).

If you are making a claim about the historical role of the institutions of science as part of human society as a whole, sure--our realization that there is a mechanistic basis for basically everything and we can understand the mechanisms led us to forget that our intuitions about how to act regarding simple impersonal mechanisms like levers do not necessarily translate to everything else.

But we grew up. We realized that there never was any reason to think about a lever the same way that we think about a squirrel. We realized that our common humanity wasn't just empty words, but reified in our genes and physiology. We realized that ecosystems are interconnected, we realized that our emotional processing systems are not so terribly different from those of other land vertebrates, and so on. We understood emergent properties. Because we understood, because we gained knowledge, we understood that our initial reaction ("oh, everything is levers, so we can treat everything with the indifference that we treat levers!") was foolish.

You claim, without justification, that "methodological naturalists set themselves the task of explaining the natural order without positing a divine lawgiver. Inevitably, in that context, nature will seem zombie-like, which makes for a dark, cosmicist re-enchantment of nature".

But there's no reason for this. The people who are actually embedded in the context of methodological naturalism tend to find nature wondrous and wonderful, they generally care about the systems they study (now that we've matured to the point where we understand that there's no reason why we can't).

It's the people embedded in the human world, divorced from nature, who are most likely to abuse it by proxy. You don't find ecologists enthusiastically recommending destruction of habitat of endangered species because "it's all zombie-like". You find real estate developers embedded in the human constructs of finance and profit and indifferent to some stupid owl--who even cares about owls?!--the ones who treat nature impersonally, heartlessly.

Science tells us that we humans are embedded in the natural world, that we depend on it, and given our power it depends on us, and humanists (see the American Humanist Society declaration I linked last time) have tended to fully embrace this view, both rationally, and with the corresponding appropriate emotions.

The effective antagonism from humans is real, but it hasn't been from methodological naturalism for decades, because people who were attentive to natural science understood through study that the mapping of attitudes towards simple machines onto complex systems (that nonetheless have mechanisms) was always unwarranted.

This doesn't mean that greed, power, and indifference in humans don't together yield destructive and hurtful outcomes. Of course they do--it's just that the scientific perspective hasn't been aligned with this for a very long time because firstly it's mostly orthogonal, and secondly, to the extent that it's not, it points out that it's wrong. For instance, students with the strongest interest in environmental issues also have the greatest scientific knowledge (https://files.eric.ed.gov/fulltext/EJ1308057.pdf).

So I think your charge isn't just misguided but actually backwards. The scientific method tells you how to understand things; understanding has shown us that those things we care about innately have mechanisms underlying them, and have replaced superstitions that can be arbitrarily discarded with the knowledge of how related things are and how interdependent life is. And scientists, as people, like people normally do, tend to develop emotional affinity towards things they understand, and rather than viewing nature as zombie-like, view it as lovely; they just better understand that which they love.