Ideas about nerfing the player’s ability to scare off a large group of Yendorian Army troops at once:

• Non-fleeing troops grudge fleeing ones (they’re deserters).
• Troops are immune to fleeing (possibly only immune to fleeing triggered by low HP, and still capable of fleeing from other causes) if they can see a higher-ranking military monster nearby.
• It’s harder to scare troops if there are others nearby (they have effectively a higher resistance).
• Troops recover faster from being scared if there are others nearby.

This doesn’t necessarily have to be only the Yendorian Army; the rule could be extended to all monsters being “supported” by other monsters of their same species, with some special cases for things like all orcs supporting each other.