If subdual doesn't mean "knock unconscious," I don't see the point of the damage type.
Subdual still means 'knock unconscious', it's just that hitting a skeleton or an unborn over the head with a friggin' war hammer should do more than bounce off them, as they do currently. (See subdual damage affecting objects, and how you had to errata that one.) As it stands I think many groups rule zero certain subdual weapons to affect skeletons\unborn\others. As it stands I'd either let them convert the damage type without the attack penalty, or just outright treat the weapon as doing lethal damage against them.
While I like the idea of skeletons and such not ever becoming unconcious, maybe the simplest solution is to have the rules say what we want to happen - that is make the skeletons immune to becoming unconcious, not to subdual damage. Then beating the hell out of them with a maul would severly impair them as per several grades of fatigued (logically desirable result) without ever knocking them out (also thematically desirable result).
the only fine tuning required would be for fatigued to indicate any further damage is lethal - wether or not the character is unconcious. THen you could use a maul to litterally pound a skeleton into bone meal .
Now, I'm not much for designing mechanics, but couldn't you do this by moving the 'subdual damage can eventually kill' bit from the damage type description to the fatigued condition description? After 'If a character with fatigued IV is fatigued again, he instead falls unconscious.' you add 'additionally, any further subdual damage becomes lethal damage instead.'
Still, I find the solution somewhat lacking, as you'd have to do enough subdual damage to cause the skeleton to fail 5 fortitude saves, and then deal enough damage to chew through vitality/wounds or cause a failed damage save. While the skeleton is fairly non-threatening by the time you begin chipping away at its vitality/causing damage saves (-8 STR and DEX and likely unable to move), it's still taking the subdual guy many times longer to down a skeleton than someone who uses a lethal-dealing weapon to begin with.