Diseases do not go away on their own. You need to use a spell, a potion, or a friendly priest (though they charge a LOT most of the time).
Vendors restock after 7 days, so most likely you just haven't waited long enough. It is helpful to get to the other couple towns, as well, so that you can have multiple vendors of each type to shop with. Makes restocking less of a chore.
Kill 'em all, let the sysadmin sort 'em out.