It's a tricky thing to view nature as our enemy. On humanistic grounds, this seems to be the presumption, but as tragically heroic as our "progress" might be, it might be short-lived and foolish. There's a big difference between being indifferent or neutral and being malevolent. Nature would effectively be opposed to our preferences only in that we'd have to assume as much to motivate our advances because we couldn't rely on nature always giving us what we want. Then again, the pursuit of our preferences might itself be unwise in that it could be counterproductive, as it leads to the environmental crisis.

So what I try to do in my writings is critique humanism on this point. Using existentialism, I talk a lot about alienation, as you say, but I'm ambivalent about the humanistic concept of progress as the taming of nature.