The real origin of the word, according to www.snopes.com is as follows. (I had to add the asterisks to get by the "bad word" editor)

The word sh*t entered modern English language derived from the Old English nouns scite and the Middle Low German schite, both meaning "dung," and the Old English noun scitte, meaning "diarrhea." Our most treasured cuss word has been with us a long time, showing up in written works both as a noun and as a verb as far back as the 14th century.

Scite can trace its roots back to the proto-Germanic root skit-, which brought us the German scheissen, Dutch schijten, Swedish skita, and Danish skide. Skit- comes from the Indo-European root skheid- for "split, divide, separate," thus sh*t is distantly related to schism and schist. (If you're wondering what a verb root for the act of separating one thing from another would have to do with excrement, it was in the sense of the body's eliminating its waste -- "separating" from it, so to speak. Sort of the opposite of today's "getting one's sh*t together.")