Putting them together with marksmanship is just... wrong.
And you wonder why I complain about mysticism. Anyway, throwing weapons do belong in marksmanship because where the hell else are you going to put them and actually justify it being there? You could make a new "Throwing" skill but that would just be a waste I think, seeing as throwing and archery, at the core of what you're actually doing, behave more or less the same. You compensate for the drop in your projectile, compensate for the power of your draw/throw, etc for both.