Getting any microorganism in a normally sterile site (blood, bladder, spinal fluid, etc.) is indeed very bad. But the GI tract is not normally sterile; we have a varied population of normal flora, and ingest bacteria when eating or kissing, just to give a couple of examples (and E. coli can be found in the mouth's normal flora, BTW, so swallowing one's own saliva may send E. coli through the upper GI tract and cause no problems). The lower GI tract is populated from the top down. Most organisms don't cause problems on their way through the tract, other than pathogenic (disease-causing) bacteria.
RodgerDodger, where was the malfunctioning "valve" in your friend? I'm guessing that somehow the "backwash" contaminated sterile areas of the body, if it reached "vital organs", perhaps through the bloodstream eventually? It sounds quite serious.
As I mentioned in the thread James cited, what medical microbiology teaches (at least when I went to school, and I'm not aware of any significant changes in thinking in this area since then) is that the mechanism of GI disease in normal healthy individuals takes place one of a couple of general ways. One may ingest pathogenic bacteria (E. coli O157:H7 serotype, Salmonella, Vibrio cholerae, for example) that either invade the intestinal mucosa or produce enterotoxins that make us sick. The other way is to ingest food that has been overgrown with bacteria that produce toxins (staph or Clostridium, for example). For more detail see: http://www.merckmanuals.com/professional/gastrointestinal_disorders/gastroenteritis/overview_of_gastroenteritis.html
All the references I've been able to find refer to the intestines as the target of these aforementioned disease process, as a result of *pathogenic* bacteria, not normal flora, and not in the upper GI tract (stomach, esophagus, mouth). It may be that ingesting a large amount of normal "garden variety" fecal flora may cause illness in a healthy individual, but I have seen nothing documenting that, what exactly the mechanism of such illness might be, or what quantity it would take to produce some sort of verifiable symptom. That's a study I won't be volunteering for, I can tell you!!!
Disclaimer: I don't consider myself primarily a microbiologist (though I did work briefly as one in a private reference lab) - rather I was a state-certified clinical lab scientist (mostly in hematology and immunohematology) in a hospital with a great microbiology department which saw pretty much everything under the sun, what with a large portion of the clientele being disadvantaged, homeless and/or immigrant: malaria, other exotic parasitic and bacterial diseases, you name it, we saw it.