I agree that having combat seem like a 'mini-game' is a problem in turn-based games, but I don't really see how a flee penalty would help. If anything it just emphasises the fact that combat is separate from the rest of the game (since, presumably, you wouldn't get a penalty if you run away from enemies before they manage to spot you).
As for henchmen doubting your abilities: if you're running away from 90% of battles, then yeah, I agree. But fleeing one or two here and there shouldn't be a problem (in fact, you'd hope your henchmen would appreciate the fact that you're not forcing them to fight to the death in the face of overwhelming odds). If they're going to complain about anything, you'd think it would be something like lack of pay, or getting too badly beaten up in combat.
