Because German and Swiss states couldn't stand up to a larger force organized hierarchically is not proof that humans have _not_ evolved to work in small groups

Because German and Swiss states couldn't stand up to a larger force organized hierarchically is not proof that humans have _not_ evolved to work in small groups, it is only very poor empirical evidence that a larger force with better weapons can defeat a smaller, disorganized force. As for why people seek freedom, I doubt most consciously think about it in those terms. You seem to think that individuals ponder about the pros and cons of going it alone or being part of a collective, but it just doesn't happen that way. When you're brought up in a culture that is already one way or the other, and that is all you know, you rarely choose because it's not even a question that enters your mind. I'd suggest reading Beyond Civilization by Daniel Quinn.