players don't like systems that punish them like this one. One of the reasons this feature is one of the most requested tweak (how to turn this off), and anyone looking for a answer can look at the Tweak thread (or VC Tweaks Tool).
devs could let it be (like Native) and don't care about balance (as the game already punishes the player upon starting a new kingdom/rebellion), but VC like BW tends more to the hardcore side, while Native is more casual friendly and easy to exploit. Besides that VC has alternative starts as a lord and king, which complicates things.
devs could apply the same set of rules to the player and AI, but that would be a big change from Native. Players don't tend to like that.
devs could apply a rare penalty for players creating too big of a army in one center. That would only be seem by very few players (conditions are rare like having the huge army, not being the marshal, etc). They went with that. Later, after feedback, they even included a warning message in the game that tells you a few days earlier that the marshall is about to get your troops, thus that message gives the player time to take them out of the center. Now, to lose troops, you need to not pay attention to the warning (a big popup message on your screen).
other things could be done like raising the garrison cost (too many soldiers in town, not enough food and ale, lots of fights, etc), thus making it hurt the player wallet instead. And so on.
