Well if they are adamant about retaining hierarchy, maybe implement a way for the ruler to "attach" themselves to the army and not actually be "assigned" the army? From the dawn of warfare up to the modern day, civilians and high ranking officials have joined campaigns, wars, and missions. Either they are considered observers, they differ to the military expertise of the one already in command, or they take command entirely.
And come to think of it, maybe certain classes in general should only be "attached" to an army and not "assigned" to it. Traders for example. Since I recently switched one of my chars to trader, I have to deal with a pesky marshal who keeps trying to order my char around. All I can tell him is "sorry, I'm 20 regions away looking for food.". Most of the time I simply ignore him though. Point being however, even though my char is assigned to the army, he's not REALLY a part of it. I think it would help for the Marshal to at least to be able to differentiate nobles he has command over, and those he has zero control over what so ever.