I understand that the top-level members of the Union view what they're doing explicitly as enforcing a specific paradigm to protect humanity from the supernatural, but it seems like most of the lower-level members believe their own advertising, so to speak, believing fully in a purely materialist reality. Social Conditioning explains why they would react so negatively to seeing something like a Son of Ether actually getting an Orgone accumulator working to the point where it can cure cancer or regrow limbs, but without Conditioning it seems like the most rational course of action for an Enlightened Scientist would be to be fascinated by this new phenomenon and try to understand it to see if it can be reproduced. After all, the core of the reason behind why Etherite technology is considered "reality deviant" is purely political, not scientific. The Union decided by fiat that it would serve their interests better if the Ether didn't exist, so they mandated that it be so. It seems like any true Scientist would instinctually balk at this sort of reasoning, assuming that they haven't undergone a Mind procedure to brainwash them into instinctually hating all deviations from Union edict.
Without Social Conditioning, I can't really see how most Technocrats would be able to justify going around kidnapping and killing people just because they're using science or phenomena that their bosses deem to be unsanctioned or "deviant".