Dear heart,
The Limbic System. Unconscious, automatic, instinctive. It's our old brain and interestingly the part that governs the whole "my god is bigger than your god" so typical of religions founded on fear.
Old and outdated science. Nobel Laureate Santiago Ramon y Cayal (1953-1934) mistakenly believed that brain cells were unique and couldn't regenerate. Hence the years of indoctrinated bosh you refer to. They were still churning it out when I was a psychology undergraduate.
In 1998 the journal Nature Medicine published a report by Peter Eriksson that demonstrated 'Neurogenesis in the Adult Human Hippocampus." Cue a paradigm shift.
I suppose these discussions rest upon what we mean by the unconscious. For some it is a metaphor, for others it is literally the Autonomic Nervous System. Candace Pert said the body was the unconscious mind. I took a shine to her teachings because she was also a woman of faith and she described us as flickering flames rather than slabs of meat. I admire people who retain that sense of wonder. She also explained how one cell bacterium are hard-wired for bliss. Nature is generous like that.
There are so many things that could be discussed. We could veer into Wittgenstein, Descartes, Descartes Error (Damasio), Damasios Error. We could explore the speculative theories on the origins of consciousness in the bicameral mind a'la Julian Jaynes, we could revel in the beautiful and assured writing of Paul Broks who presents case studies of those who've experienced brain trauma and the "reset of their personality dials."
Ultimately though this whole debate hinges on whether we accept the freudian model of the unconscious (1915) as a cauldron of primitive impulses along with his take on the structure of the psyche and the need for defence mechanisms or whether we choose to reject it either in favour of something like Wilson's adaptive unconscious (2004), or to reject it completely.
Rousseau or Hobbes? Forgive my feminine sentimentality for I'm a romantic. I like wine, music and song. I will always prefer poetry and mystery over facts and hard science but I don't find my faith or sense of awe is diminished by the explanations of those who look more closely. Instead I find it enriched.
I am pagan and am quite used to the feeling of others trampling over my faith with man-made ideas so I do sympathise. I shall close with one of my favourite quotes from one of my favourite authors:
"Oh what a catastrophe, what a maiming of love when it was a personal, merely personal feeling, taken away from the rising and setting of the sun, and cut off from the magic connection of the solstice and equinox. This is what is the matter with us. We are bleeding at the roots, because we are cut off from the earth and sun and stars, and love is a grinning mockery, because, poor blossom, we plucked it from its stem on the tree of Life, and expected it to keep on blooming in our civilised vase on the table."
~ D.H. Lawrence
Or as Freud simply stated, "Civilisation is madness."