All the constituents and actions are governed by universal natural laws and an immaterial entity like God cannot create a material entity like the universe.
The question of how these immaterial entities can act upon material entities is deeply involved in what is generally known as the mind-body problem.
O'Brien and most of the other native Federation people didn't seem to worry about spiritual matters much; troubles of the soul and concerns about immaterial entities didn't interest them.
Qualia-based arguments: Some philosophers see the existence of Qualia (or the hard problem of consciousness) as strong arguments against materialism and therefore for the existence of material and immaterial entities.
Not to the People directly, of course; the Company was an immaterial, omniscient, omnipotent entity that, except in the matter of punishment, dealt with People only through Company Agents.
According to Platonism, the One or "first cause" radiated immaterial and material entities in a hierarchical, categorized way.
What distinguishes alchemy from these related traditions is its unique view of the elixir as a material or immaterial entity that represents the original state of being and the attainment of that state.
Buddhism does not deny the existence of "immaterial" entities, and it (at least traditionally) distinguishes bodily states from mental states.
This event will of course allow the stasis of time to collapse and the imprisoned immaterial entities will be liberated; in precisely the same condition as in the instant of their encapsulation.
These malign immaterial entities forever seek to breach the material universe and subjugate or consume all life within it.