Good ole molecules actually *do* do some weird stuff and screw up your nicely-planned tests! Read NewScientist or some other science-related magazine and see how often people are surprised by what happens! :-)
As far as investigating the phenomena that constitute consciousness, that's what all the barrels-down-rivers experiments are looking at. The problem is that since consciousness covers so many areas, the only structured way to hit the problem is to deal with each area in turn. And from there, the only way to investigate each area is to find what it does under a load of different situations, including ones where it gets bogus data or carries out bogus operations (either by injecting bogus data into a healthy brain, or with the assistance of someone whose brain naturally produces bogus data or operates incorrectly). Hence the experiment in the original post.
Physical phenomena aren't the only way of tackling consciousness, of course - sometimes the river goes through that metaphorical cave, in which case the challenge is to get lots of people to do the same thing and see what works. I do tai chi, and I'm well aware of the theories about chi "flow". I'm also aware that they're no more than exercises in visualisation to promote relaxation and hence faster movement, or exercises in muscular mechanics to give a more powerful/flexible/resistant body position, but it doesn't mean they don't work for me or other people. Our tai chi instructor is also using techniques from neuro-linguistic programming, which are scientifically-derived procedures from studying how consciousness responds to inputs. There have been (and will be again) studies in using hypnosis and visualisation to control pain from real bodily damage such as in surgery. Not to mention the placebo effect, which is the reason for controlled trials.
If you want to call this aspect of investigation "spiritual" then OK. The problem is though that the notion of duality requires a dividing wall - *this* is physical, *that* is spiritual. So far, all attempts to build such a wall have resulted in the train of physical science ploughing straight through it. Whilst we might not yet be able to do any controlling in many cases, the various scans possible on brain function make it clear when things are/aren't happening, giving definite physical input and output. So I'm afraid I can't see how your attempt to build this wall will be invulnerable to the oncoming train.
Certainly I don't see that your idea about doctors "invalidating" people who've had OOB experiences are a reason. What "creative insight" could you see arising from this? Sure, all medical staff are trained to be positive around patients, because a positive mental attitude helps recovery. But beyond that, what purpose does sustaining the illusion serve?