Again, I have to stress that it's never about what but how you do things. If your story dictates that a character must die, that character will need to die, whether it's by the player's hands in battle or by some story action. Obviously, when planning such a thing at the design level, you might put in a story branch that predetermines the outcome to the player killing the target if you're hellbent on bloodlust as a designer. However, what really changes if an enemy general is killed? Does that army not have a chain of command to fall back on? Is their military complex hinging on that one character? Sure, we'd like to think one person can make the difference, but the story isn't about the general's actions unless they're a secondary character or a primary antagonist. In which case, you'd make a story branch or resolution, but it's crazy to suggest they're all so important that this system would need to branch that much to stay in line with the story. They may be alive or dead, but, again, unless that aspect is in stark contrast to your story, you don't need to create a story branch. I don't know if you looked at the conversation code for events that I detailed elsewhere on this board, but you can ignore a character's lines or a whole conversation depending on some condition (like PlayerName.IsAlive), and this could certainly be used to put a new general into the mix.
Brute force isn't always an option at higher difficulties. In fact, losing and retreat are always options, since you won't always be able to win by just throwing all your troops until everything is dead at higher difficulties. I find it hard to believe that no one, over the course of the entire game, would look at a main character's actions, have the resources to plan to appropriately defend against the character, and then simply not do that.
As for lacking the quality of fun because of choosing the "most efficient" route, that really says a lot about the player. Maybe they just shouldn't be playing games? You'd really poison everyone every single time if it was faster (and the condition of access to a water supply was met)? Even if everyone in the game decidedly hated you and insulted you at every point (massive negative in Total Humanitarianism)? Maybe even the blackmarket people and domestic animals wouldn't want anything to do with you. The engagement here, by comparison, is that you're playing by a standard, instead of the bogus maniacal standard, "If it moves, it must die." However, most of the options can be achieved in the context of the battle system.
As for feature drift, this is a design to be part of an engine. There's no such drift in a game. There's just the choice at that level to decide what to include. If you don't want anything from this, you don't have to bother with it (force brute force and call your own formation screen state). Remember, the engine is state-based, and you control that, meaning you could have a game that never bothers to even call the battle state.
Offering different missions (re: mission variety) is not the goal of this system. If the story says, "The character takes over Fort X," then you're taking over Fort X; that's your mission. It's just how you do it that changes, which still falls into the context of the battle state, regardless of the option at the planning level. Let's say you try to negotiate, arranging a meeting on the field. When they invariably turn you away, you might think, "Oh, well, it's time to brute force my way in. I should have done that from the beginning." If they have the manpower (or gates that lock from the inside), you won't be able to accomplish the story goal. You'll need to retreat and pick from the options you have left. If someone gets frustrated that a game is "unfun" at this point, even though they're being engaged by the system to solve a critical thinking puzzle, then they can switch difficulties and devolve to brute force for the rest of the game (which strips out the critical thinking/tactics). Example.
The character takes over Fort X by...
- brute force (single company).
- concerted force (single company, but as many units as paid for).
- pincer attack (2 companies).
- back attack (single company).
- ambush (2+ companies).
- feint (2 companies).
- clear and hold.
- air strike.
- box-in maneuver.
- turtle maneuver.
- cannon volley.
The sentence will still read basically the same way: The character takes over Fort X. Story branch before that if you want a different goal. Story branch after that if their choice of how somehow managed to be out of line with the story.