HIV-can remain dormant a decade or longer before causing AIDS. It wouldn't really be noticable as a disease until it manifests, though, right? And how many turns would a decade be?
Untreated syphillis...yes...it will produce horrible problems...but over a long time. And folks are still very functional for quite a while. Years and years and years. And their eyes don't pop out. They don't develop chest wounds, etc.
Actually, I would like to see these diseases be more along the lines of diarrhea and the like. Disease often killed more people in wartime than combat did. So adding it in is realistic. It's just that there aren't any diseases I know of which have the characteristics of even the nonmagical diseases you get with Dom 2.
I think the uncertainty factor with diseases would be very interesting.