I agree with your sentiments and it’s not as if the “hierarchy of being” system is free of mysticism and magicalism. It seems to me the problem is with immanentism and not just Hegel himself.
I don't see the great hierarchy of being as a "system" at all — unless by "system" you mean "universe" or "cosmos," and not its narrower sense of a philosophical doctrine. Rather, I see it as a simple description of the universal context in which human beings exist, thus comprehensively forming the irreducible bases of human experience.
On this view, to put it crudely, human experience only comes in these four "flavors," God, Man, World (natural world, physical world) and Society (community, polity). You can test the description for yourself by engaging in a simple exercise in self-awareness. Pick any ordinary day, just go about your regular daily routines; but while you're doing that, try to reflect on the types of experiences you are having involving any "other than yourself." If at the end of the day your experiences involved anything other than experiences of these four "partners" singly or in some combination, then I would dearly love to know what that was.
Of course, if you think the God partner is mystical and magical per se, then probably the description of the great hierarchy of being is senseless to you. But this result would be a function of your predisposition of unbelief.
Which brings us to the man "partner" and his relation to God. Perhaps the greatest insight of classical Greece and of Judeo-Christianity is that ultimately, it is the God–man relation that is key to the good order of man and thus of the justice of his relations with other men and with the other partners in being.
The French philosopher Henri Bergson spoke of the man who lives in "openness to God" as l'âme ouverte, or "the open soul." There is also the man who freely chooses to close his soul to God, the l'âme close. The idea here is that the man who closes his soul to God "deforms" himself. (I'll spare you the details for now and just mention that the good order of the soul in open existence under God was perhaps Plato's major preoccupation over a long and prolific life; and that the "turning around" of the soul (e.g., Plato's periagoge, or the Christian "born-again" experience) to Christ — the Way the Truth and the Life — is the divine remedy for such deformity.)
There are echoes of the great pre-Socratic philosopher Heraclitus in Bergson's insight. Heraclitus maintained there are only two types of men, the "public man" and the "private man."
The public man — the mature, wise man — is such because he acknowledges the Logos, or the universal order of being. He sees it as "one and common" and thus binding on all men as the true source of order not only of the individual human being but of the good society. Thus the public man is a man who is "awake" because he understands that the order of the real world is "one and common" for all men. But there are others — the private men — who, not acknowledging the Logos, are in effect "asleep, each turn[ing] aside into their private worlds." They live "as if they had a wisdom of their own."
The analogy to Bergson is that Heraclitus' private men are cases of l'âme close. WRT the private men, the "many," Heraclitus put it this way (Fragment 1):
Although this Logos is eternally valid, yet men are unable to understand it.... That is to say, although all things come to pass in accordance with this Logos, men seem to be without any experience of it.... My own method is to distinguish each thing according to its nature, and to specify how it behaves; other men, on the contrary, are as forgetful and heedless in their waking moments of what is going on around and within them as they are during sleep.The l'âme close, by not acknowledging the Logos, falls asleep into his own dream world, and thus becomes a private man. It is out of that dream world that all Second Realities arise....
Some things never change.