You could cushion as Drew suggests, but cutting down the neck support is very easy. There is one screw on either side of the outside of the case: right next to the handle, and exactly opposite on the other side -- these correspond to where the neck support sits inside the case. Unscrew these with a phillips head screwdriver, and make sure not to lose them. You may have to cut the plush liner a bit where the neck support meets the floor of the case, I don't remember, but then you should be able to just shimmy it out. There are a couple of staples on either side that will try to keep it in there for you, but gently pull the support away from them. The support itself has three layers - a core of styrofoam, sandwiched between some balsa wood, and then the fur liner. Peel back the fur liner, and use an exacto knife to cut as much from the foam/balsa support as you need (1/4-1/2 inch will probably do it,) and then slip it back into place. If the staples are still poking through the lining of the case, you'll have to gently ease the support in place. Then screw it back in, and you're done. If you left extra fur on the support, you shouldn't be able to even tell you performed the surgery.
Good luck!