As I explained before, even if you set protections, thats not the problem on your kerbal.
The problem is, if he is not part of the ship, its calculated as "something else", and thats the problem. the only solution I see is somehow make it part of the physics of the ship, and the only way i know for such is, to set it on a leather.
or may be have several command seats so it can jump from one to another (but I am not sure that will work). I will test both theories later.