Even though this might be half of an essay, I think you hit the nail on the head regarding the essentially unnatural fit of Markus as a leader. This is part of what made Jeremiah a unique take on the post-apocalyptic genre, as a lot of the shorthand normally employed is missing. Survivors in typical end of the world scenarios take fitting roles to their experiences and temperaments, and Jeremiah is, as you say, about a "proto-society" in development as opposed to the remnants of a previous one.

Besides being food for thought, I also just completely enjoy this essay as a character sketch.