Keith,
Yes, that's it exactly. It has to do with the domestication of the
animals and the host opportunity this presents for viruses -- not the
health of the animals per se.  The doctor seemed to suggest as much when
he referred to this being common among game animals raised for food, and
he was aware of several Canadian studies that confirmed this.  They were
unable to conclusively identify the particular virus I had been exposed
to -- it wasn't CMV, but something similar.  If I eat raw organ meat,
even if marinated 12 hours or more, I still get a mild short-lived
recurrence of the symptoms.   So my advice is stay safe and cook your
meat.
~Eliot