Your question is relevant to any RPG and not just Mouse Gaurd.
Generally speaking, unless the PC’s have a major role in leading the battle, I don’t involve them in command of the troops and don’t run the conflict simulation of the battle on the PC’s side of the screen. In Mouse Guard terms, that means that the PC’s are directly involved in choosing strategy or negotiating the results of the battle unless they planned and led the battle.
Instead, what I’ll tend to do is treat the battle as if it were an adventure with a series of challenges within it, where the failure or success of the PC’s during those challenges not only bears on their personal outcomes (whether they survive the battle or not), but also has some bearing on the outcome of the battle. Whether you decide to test the outcome of the battle or just decide how it ended really is a personal choice there.
So the question comes down to did your patrol of mice actually plan and lead this battle, or are they simply participants in it? If the patrol leader is planning and leading the battle, then regardless of whether one of your PC’s is too young to be leading the battle, they should have a leading role in it and you should run the ‘war challenge’ with the PC’s narrating their actions and tactics within it. This narration can be like the “mix of the two” you are thinking about, where the patrol leader issues commands in the battle and your young PC is playing some critical role in critical moments in the battle.
If on the other hand all the PCs are merely subordinates themselves, then IMO you should focus on their ground eye view of the battle entirely. Not only will this feel more natural, but as your PC’s evolve to greater responsibility this will be reflected by the game you are playing so that the players will actually feel their progress in a very direct manner.