All you will have to do is:
-Get a moving blanket (or two) and drape them over the front of the bike.
-Get a Tarp and bungie cords and cover the bike (or buy a snazzy Bike Cover)
The moving blankets will act as a 'bullet proof' padding under the tarp (or cover). This should protect your bike from all but golf ball sized rocks (and if they are that big there are probably more problems going on).
I did this with my harley on the back of a small flat trailer. No problems after a 1900 mile trip...
Worth a shot.