I've read a suggestion that you pack the area of the case surrounding the headstock tightly with crumpled newspaper (or whatever) to prevent that "whiplash" effect. Assuming that the body/soundbox fits snugly in its part of the case, it shouldn't be necessary to immoblize every inch of the neck between the headstock and body, as long as the guitar is held firmly in place at both ends.

That said, I haven't tried this approach myself, nor do I plan to. As a rank amateur, I never need to take my guitar on a plane trip, since I'm not flying from gig to gig nationwide (or worldwide). The only way I travel with my guitar is when I'm driving.