On one or two occasions I was overheard discussing Marine Corps lore with other boots, and corrected by one or more of the old salts. In particular, I was told that the term Jarhead originated in the Corps back in the days when mules were still used. As anyone who has ever watched an old western movie knows, mules were often referred to as Jughead. The oldtimers insisted that Marines also referred to their mules as Jughead and/or Jarhead. Over time, certain stubborn or hard to deal with Marines were also called Jarheads.
There it is, take it or leave it. Myself, I can accept the above as the origin for the term Jarhead, and still see how the newer explanations also became attached to the legend and became the sole existing explanation. We May never know for sure.
http://www20.brinkster.com/gunnyg/jarhead.html