He clearly states he thought your central point was: "It will always suck to work for large organizations, and the larger the organization, the more it will suck," because "humans weren't meant to work in such large groups."
How is this so different than your stated thesis that: "the central point is that in an organization organized as a tree structure, structural forces tend to give each person freedom in inverse proportion to the size of the whole tree. That we work better in groups of 10 than 100 I feel is obvious enough not to need justification?"
His refutation relies on examples of humans partaking in behavior that they were not originally "evolved" to do. It is a direct response to your reliance on evolution. If you thought the whole point of your essay was "obvious enough not to need justification," then why did you write a whole essay on the subject?
To address your central point, I would cite the space program. Humans were obviously not evolved to be space-faring creatures, and yet hundreds (thousands?) of human intellects in concert (in a tree-structured organization) managed to land a man on the moon. The idea of synergy, where many humans in an organizational structure can accomplish more than any single human's evolved capabilities, has long been recognized (http://www.complexsystems.org/magic.html). Many people that work in such organizations draw personal satisfaction from the fact that they are furthering what they consider a greater good, rather than their own personal desires. Where a start-up glorifies individuals, organizations tend to glorify the whole. The fact that this is not satisfying to some does not mean it is not satisfying to others, and certainly does not imply that “You were not meant to have a boss.”