I personally would just keep fly spray on it and let it heal on it's own time. Let it scab up and heal without messing with it too much. Of course, keep an eye on it for any signs of infection but that is a fairly minor injury and should heal up with no problems.
You may not need to use shipping boots. If he has never had to back out of the trailer before, it is only natural he would be clumsy and uncomfortable about it. Just work with him on it so that he backs out comfortably and slowly and you probably wouldn't have any more problems.