I am not aware of anyone who has taken Kaczynski seriously enough to do academic work on his manifesto. "It is hard to deny the brilliance of the man". No this is not difficult at all. The manifesto is a lot of declaration and generalizations, and appears to be little troubled by anthroplogy, sociology, or psychology.
In general Kaczynski's perspective is representative of the Luddite inclinations of Romaticism, which treats any change from the way things were in an idealized past as a negative, leading to hostility to technological advances. Romantic Ludditism is an attitude that humans fall into easily, and one can find similar decrying of basically every technological advance in history, throughout history. Note, humans are intrinsically dissatisfied with their lives. This is not a unique feature of the industrial age, unlike Kaczynski's delusion.
The refutation to romantic Ludditism is through anthropology and sociology. Humans pre-technology were at great risk from starvation, predators, and disease. And the needs of a hunter-gatherer lifestyle were so time-consuming, that there was no time for the development of the sort of knowledge that Kaczynski articulated -- there was no philosophy 200,000 years ago. Nor writing, etc.
Humans developed technologies of tanning, pottery, twine, adhesives, fletching, etc, and made homes, storage vessels, clothing, and weapons. This technology made life better for the inventors for a time, until the Darwinian process of population growth drove humans further out into what had previously been uninhabitable regions. Tech assisted hunter-gatherers were able to live almost anywhere on the planet, but life was not GOOD. They were far less at risk from predators, but no more secure from starvation or disease. And humans have always preyed upon each other. ~15% of hunter-gatherers died from human on human violence. Life COULD have been idyllic in an under-populated and rich hunter-gatherer environment, at least when disease or other natural disasters weren't messing with it. But humans only transitorily lived that way, they overfilled their niche, and starved, and fought -- and the phenomenon of a gang or pirate boss is typical of how our natural social system operated. Life was not idyllic for tech hunter gatherers.
Note that Kaczynski treats an underpopulated time as representative of what pre-industrial society was like. His model was frontier America, where an early industrializing society, with its massively larger potential population densities and much better weapons, had driven lower technology native American societies off the land. This was the transitory "happy" times for pre-industrialists, when population had not yet risen to its sustainable limit at that tech level. Note, Kaczynski declares all pre-industrial people to be psychologically healthy -- using as far as is discernable from his manifesto -- rose colored glasses as his "research" tool into the psychological health of frontier Americans, and every other pre-industrial culture he cites.
The development of agricultural technology was transformative, as the population that could be supported per acre from agriculture was many times that from hunter gathering. This did not end warfare, or disease, or starvation, though. What is DID allow was the development of a small educated class, and writing, and the process of knowledge accumulation that eventually lead to science and modern medicine. It also lead to caste systems with an inherited boss class, and professional armies to maintain that boss class in its advantaged status. Life was not idyllic in agricultural societies.
Modern industrial technology has given us the capability to limit our population growth, which is critical to keeping a benefit from technological advances. It has dramatically increased the size of the educated class, allowing more than just a few priests and warlords into the ranks of those who debate our potential paths forward. It has enabled the development of modern medicine, so that debilitating injury and disease, plus devastating plague, are no longer likely life paths for many. And the democratization of public discourse, has lead to the gradual moral improvement of human attitudes as a whole. The Better Angels of Our Nature is an outstanding compendium of that gradual transformation, leading to far far less murder and warfare today than 20,000 years ago.
Kaczynski would have been far better off referencing the Gaia hypothesis, and studying Deep Ecology, than his Romantic Luddite illusions. Gaia is not able to reason, nor does she have the technology to protect the biosphere from external threats. Humans, as the reasoning element of Gaia, CAN study the threats to Gaia, and develop the technology to mitigate them.