It's better to not think about biology as software vs hardware. Also, most diseases would be hardware defects in this metaphor, so why would fixing hardware not help? If you can treat a brainless person for the disease (we do that, e.g. if a mother is bearing a child, we might keep her alive even though she is brain dead), there shouldn't be any problem with using decephalized humans as models. Placebo effect works (e.g.) by tricking the immune system into action (doable in a decephalized human just as well), not by telling the disease to go away.

The assumption that most diseases are hardware is that, an assumption.

Some may be, sure.

But could it be that a blanket claim like that comes from us already knowing how to access the hardware, and being uncomfortable to wander out of that comfort zone?

Of course you can’t “tell” the disease to go away any more you can tell a bug to take a hike, but saying we can manipulate the hardware to trigger whatever immune, etc. responses just as well comes from that being the thing we can sort of do reliably at this point.

And even then, can we really?

Read about the phenomenon of cascading medical involvement during childbearing and birth: turns out “hardware manipulation”, which is very compelling to do, tends to have compounding hidden consequences, while the adjustments in the elusive “software” (inducing relaxed state etc.) somehow appear to yield straightforward results. Again, immediately life-threatening conditions aside.

Manipulating transistors and condensers (triggering an immune response, in your example) might just be a suboptimal, incomplete approach when compared to updating the firmware logic (making it so that the response is triggered when and how needed), or of course better yet both.

Our discomfort with the associated uncertainty, however, makes this an unfashionable direction of scientific exploration.

This is exactly where the software/hardware metaphor breaks. The software is the hardware, and the hardware is the software. The mind is - not influenced, it simply is exactly that - the processes in the brain, and the body acts on various kinds of signals sent by the brain and vice versa - and we should be perfectly able to simulate these signals if we can grow a brainless human body, and see the effects on the body. That would help us a lot in determining what needs to happen within the brain and in turn within the mind, for example, if said problem is psychosomatic or mentally fixable. However not everything is driven by the brain - and treatment for stuff like most types of cancer has nothing to do with the brain at all, same goes with vaccines development, stuff like Crohn's disease etc.

Let's say it's possible to trigger immune response by focusing really hard. Still we need the brainless human to determine which signals the brain needs to send before we start trying to get people to focus really hard.

We disagree at the unfalsifiable “mind is the processes in the brain” conjecture that you stated as an axiom.