I get that you prefer autonomous allies, but that's your main reason for backing it? That's like saying I bought Fallout because of their barter system.
I cant see how the barter system in fallout was as promising as having uncontrolled allied NPCs (uncontrolled in combat as they aim to provide general directions to NPCs before combat)
It is a compelling game design choice that ensures that they go a certain direction.
The game is (supposed to be) about survival and leadership. Uncontrolled characters open the door to a quality feedback on leadership.
It also warrantees they can invest developpment time on certain features without fearing the player does not see them.
You are on a good run, being successful at expeditions:
controlled characters: you dont care. The morale aspect of your allies is secondary as you control them fully. No matter how hard combat is, you can game the system. Feedback on leadership does not matter.
uncontrolled characters: you must capitalize on the good morale and trust your allies grant you. You must aim higher than usual in order to secure some few days in advance.
You are on a poor run:
controlled characters: you dont care. You can game the system and you do not have to fear poor reactions from your allies, the commandment chain being perfect.
Uncontrolled characters: you must factor in the start of loss of confidence your allies have. They might reveal less reliable than you think. You have to think of the situations they can endure. You might have to bargain with other groups in order to get items in a secure way, to rebuild the morale.
Uncontrolled characters: a near certainty allies are going to flee or die in combat.
You can invest on features like returning to camp after fleeing combat. It might create friction with those who remained solid in the previous combat. They might ask the leader to expell the coward. Dead characters, survivors might ask for explanation etc You can invest on developping all these features because you know players are going to struggle to game the system.
Uncontrolled characters warrants a quality feedback loop on the leadership. The coders can spend time implementing an expert system to analyze the leadership because they know the players are going to struggle to game the system. This opens the doors to contextualization of decisions taken as a leader and assessment based on the results following these decisions.
Randomization of loot will ensure that no run is acquired as you might do things well but run out of luck.
Etc…
Quite a fruitful compelling game design decision.