I don't really see why the 'flee' mechanic should have a heavy penalty attached to it.
I guess there's no real reason. Why do you think there shouldn't be a penalty? I just think it would be one way to make combat actually part of the rest of the game, instead of being a separate mini-game like it is in many games.
In many turn-based games, for example, you go into a tactical battle with the units you have amassed at the strategic level. The units you lose in the battle are lost forever in the strategic level, making the battle more a part of the game.
In many RPGs you just give your dead guys a Phoenix Down or get auto-resurrected after a battle. In some games someone might pay you 2000g to get rid of some ghouls somewhere, but after you've done this you can go back there again and see the same ghouls patrolling the area as usual. So you actually, really didn't affect anything.
They already have permanent henchman death, if I remember correctly. That's one way to make combat meaningful. As a henchman I would seriously start doubting your leadership and tactical abilities if we were just running from 90 percent of the battles we got into. I would *certainly* warn all my henchman-friends about your disregarding behaviour. Like you were treating your companions as disposable units in a game!