Well chakra certainly isn't a new concept. Though this iteration of it is greatly fantasized from spiritual power centers in the body.
Is it physical? yes and no. Certainly if your body is not well or injured the spiritual power will be effected, and vice versa. But could a poison be created to disrupt the ability to wield this power?
Hmmm, well we now have the whole Kagura and her son's origin for its wide spread usage. And in that we are told that instead of using our spiritual energy to connect with one another, we combined our spiritual and our physical energy to make and then use chakra as weapons, totally screwing up the whole concept from the get go. Go humans.
We are also told that the energy is created in chakra coils that surround and connect together our chakra producing organs. The physical energy[increased through training, stimulants, and exercise] is collected from each of our cells, while the spiritual energy[increased through studying, meditation, and experience] is collected from that produced by our consciousness. Maybe attacking the physical half of chakra production is possible...tainting the cells in such a way so that physical energy collection fails and it is not stored for use. Changing the make up so that the body attacks this energy with an immune response to kill it. Disrupting the ability of the cells to give up this physical energy for harvesting. We are told that now, without chakra, the body will die. Yeah evolution!
I would think that it would be possible to create a specialized poison that would disrupt the physical energy production and possibly the spiritual as well, though I would not accept a physical poison for that unless it was specifically crafted to attack the consciousness. And once you have someone unconscious why waste time with the chakra anyway when they are helpless to react anyway? Nice rock to the skull should suffice.
I am leaning toward saying that you could disrupt the physical energy production, taint it enough to cease the production of the combination of physical and spiritual for chakra production, but that you would not be able to alter ones ability to just do pure Ninshuu as intended by Hagoromo. But how many SL nin have bothered to learn that at this stage?
I know of maybe 3, Athos, Warren, and Mai to a very limited degree. there may well be more out there.
If that poisoner in question, Bocchiere, did not specify the how in these precise terms but is just saying it works cause, then I would not buy it in the least. And I have had to stretch quite a bit here to come up with a semi-half assed notion as to why it might work in the first place.