I agree it's completely nonintuitive, but just from this conversation it seems pretty clear that there's no significantly superior or less ambiguous way.
The only instance in "everyday" usage where I would use my thumb to point would be to point to someone behind me, over my shoulder (and that's not even a directive to go in a particular direction). I doubt that's where it comes from, but I found one thing that makes it more "intuitive" to me is to always accompany the gesture with a "back and forth" motion along the axis of the thumb - that way it looks more like a pointing gesture and less than a "yeah baby" sign.
The only instance in "everyday" usage where I would use my thumb to point would be to point to someone behind me, over my shoulder (and that's not even a directive to go in a particular direction). I doubt that's where it comes from, but I found one thing that makes it more "intuitive" to me is to always accompany the gesture with a "back and forth" motion along the axis of the thumb - that way it looks more like a pointing gesture and less than a "yeah baby" sign.