I'd be really, really careful with this, though. We saw in Star Wars Revised the problems of allowing certain attacks (in that system, critical hits) to bypass hitpoints and go directly to wounds. To whit, it made the system almost stupidly lethal (Gary Sarli did a great post in the lead-up to Saga explaining the average party life-expectency under the old system only accounting for one-shot crits; including the other ways of dying [like being normally run out of hit points] were completely separate and would have added to the odds of dying]).
Letting crits bypass hitpoints was definitely a mistake.
In general, anything that might apply to "hitpoints" needs to scale with level to account for the general abstractness of hitpoints in that they increase due to skill, training, luck, etc. Assuming wound points don't scale with level, they're obviously measuring entirely different things; it makes no sense to allow an effect that does lots of hitpoint damage (representing its ability to seriously affect even opponents of significant skill) to therefore inflict particularly serious wounds.
If sneak attack damage applies to wound points, it may not scale.
At this point we'd have somewhat resolved the survivability issues; but it's still a bad idea to include bypassing effects commonly. It's going to be hell to balance for one; suddenly rather than working together; the fighter and the rogue are working against separate clocks. Very commonly, that'll mean that in some scenarios the fighter might as well give up; and in others, the rogue might as well twiddle his thumbs, depending on the ratio of vitality points to wound points.
It's OK for PC's to excel at differing tasks, but that's pretty extreme. Not just that, it takes away a key point of D&D combat, namely party cooperation. With that mechanic, it's actively harmful to cooperate and focus fire; you're much better off each focusing on your own opponent. The idea that the fighter might engage and the rogue use the distraction to flank would be dead; after all, any enemy the fighter's already engaged is likely going to die of hit point loss before the rogue can kill him (assuming they both are roughly balanced). Or, if the rogue can still get the kill faster despite the fighter's head start, he'll be rightly asking himself what exactly he's contributing - why not play a spell caster or another rogue since his strong melee attack is irrelevant?
So the problems you point out in terms of survivability are compounded by problems in gameplay.
The key win of a wounding system shouldn't be trying to distinguish what type of attacks can wound and which cannot, it's that healing feels more natural. Of course you can let some effects exclusively to vitality points only (say, damage on miss), and you can let others deal wounds directly (say, coup de grace) - but those should be exceptions, not the rule, otherwise you'll mess up balance, survivability, gameplay... and I bet it'll result in ludicrous corner cases problematic for believability too.