I agree on both points. It seems that Traveller is intended to model things in a non-supernatural way, so that the supernatural has to be more scarce than psionics, even, or else the game really loses its Traveller feel... and becomes more RuneQuest-like, I suppose.
Perhaps the next step is to expand the Totem concept into a full-blown pantheon of little gods, which would further differentiate psionic and magic effects between the various adherents. Eagle totem, Bear totem, Orca, Thunder god, star god/spirit, dryads, god of the Mountain, god of Jumpspace, Oyarses, eldila, fire/air spirits, war god, peace goddess, etc.
The fun starts when one tries to reconcile this increasingly strange TU with the OTU's historical roots, i.e. in Terran history. The Interstellar Wars, the Terran Confederation, UNSCA [sp], the World Wars, the British Empire, the Enlightenment, Dutch East India Co, Ming Dynasty, Ottoman Empire, Aksum, Ghengis Khan, Charlemagne, Mohammed, the Gupta Empire, Ardashir, Rome, the Christ, Asoka, Siddhartha Gautama, the Nubians, Alexander, Solomon, the Minos, Mohenjo-Daro, Sargon, Egypt, the Sumerians...
I suppose the trick is to posit a diverging point: just as the Tech Level tree seems to move the "quickest" in the center and "slowest" at the ends, perhaps materialism and deism are strongest in the center (TL 4-A), and the various forms of interactive theism are more vibrant on the ends (TL 3-, B+). So at some point in time, when Tech Level advances start stretching out, the supernatural has more obvious influence on people.
I dunno.