Nearly three years ago, in this thread, I gave ideas on how to implement infectiuos diseases; I will now try to give ideas on how the player can react with them, and some of these ideas might have to be implemented first, meaning my suggestion will be implementer no sooner than 2018 or 2019 at the soonest.
First, doctors should be able to diagnose creatures infested, especially among migrants and imported animals, and, if the disease is unknown by their civilization, they should be able to study it and record it in a book, further enriching the mountainhome, similar to animal training.
Second, and since quarantine has been known before 1400, with the Hebrews ordered to isolate "lepers" in Leviticus and, nearer from the cut off year, a 1377 statute in Ragusa ordering newcomers to spend 30 years before entering, doctors should be able to order the isolation of known contagious carriers to special zones in the hospital, or simply left to die in a pit. Maybe the doctors would have to wear specific dress such as the plague doctor costume to reduce the probability of being contaminated.
Third, as for the cure, doctors would have to heal the symptoms (giving antipyretics to a patient with fever), the consequences of the disease (cutting off parts with necrosis) or sometimes the disease itself, the latter having to be rare enough because of Medieval stasis but not too rare to make the game too much difficult. It would need the implementation of
drugs and medicine.
Lastly, in order to bury the deaths from outbreaks, mass graves would have to be implemented, with one square containing five cadavers (more about funerals
here).
The diseases I would choose to put into DF would be the plague, tuberculosis ("white plague" or "consumption"), typhus ("gaol fever"), measles, variole, malaria, sleeping sickness, influenza, leprosy, dysentry, yellow fever, poliomyelitis, rabies, mumps, a generic hemorragic fever, rubella and cholera; I would add the fantastic diseases of elven plague, gnomepox and other diseases generated for deities, demons and angels to punish entire communities.
As for the point about the interaction framework, I just wanted to propose something which would be more straightforward to implement and more specifically geared to the subject.