I don't understand the controversy. We know full well the natural world is full of substances with significant impact on our bodies. Many such substances can even on average be harmful, but when used correctly, they are beneficial. Opioids come to mind first and foremost. It's not controversial to give e.g. serious accident victims a shot of morphine. Why are investigations into medicinal use of shrooms or marijuana…
Playing the devils advocate, and I think this is a pretty strong point against shrooms: while opioids cause harm, their harm is incredibly mechanical (it’s just addiction) and can be managed well. Shrooms play with your brain. We barely know how that works and quite frankly a lot of the research into managing the depressive episodes with shrooms may just be that you become more stupid and therefore less prone to thin…
Of course opioids play with your brain. So do SSRI antidepressants for example, whose very name is based on their most commonly accepted mechanism of action. And it's not only strictly psychiatric drugs—ADHD medication also plays with your brain, influencing dopamine pathways. But then so do gambling, and physical exercise, and meditation! Heck, even social media plays with your brain.
The mere fact that something has an effect on the brain is not in itself an argument against it—let alone when it is being proposed as a psychotherapeutic tool.