Let me try saying that again, a different way.
I recognize that there’s story about a player-as-protagonist; that is the problem. The narrative copy and the characters actually in the roster and appearing in the field creates a continuity problem for the reader/player that can only be resolved by assuming “I” am not a warrior, but rather a lead-from-behind sort of manager. Or as you say, lead from the sidelines. That is, the game restricts us to a view of ourselves that–in the context of a story about warriors–is fairly unappealing, the protagonist-cum-football manager, or the Battle Bureaucrat.
Most of the games in Battle Brothers’ genre avoided this the cheap way, i.e., by not describing the player as a part of the group at all. The player as an invisible guiding hand with the characters in the game as the protagonists. We’re then free to weave any story we like about the intra-group hierarchy and relationships. Given the extreme control over each character, that often makes sense and would make sense in Battle Brothers. I think that would a reasonable and cheap change only affecting the already written copy, which would completely resolve problem.
I think a better solution for the player, but with a more costly implementation for the developer, would be to allow us to chose one character to represent us. To make this palatable for people who aren’t into permadeath games, I suggested the selection could be optional and possibly upon death the player could choose a successor. I would welcome a game where the death of the protagonist was the end of the game, even though such a thing has never been done before.