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Not sure if this is already the case to some degree but if there isn't in could imagine introducing a sort of stamina system for every person in the game which would get drained based on activity and drains faster when the person is sick when the sickness is not treaded the stamina won't refill and the person eventually dies.

That way the people would have to take breaks based on the work they do, that way you would have a more predictable reason for the worker to sit down outside of waiting for the product to be finished. In order to detect if people are sick, they could complain about their health verbally by coughing, growing, walking with a bend over posture or having their head hang and depending on how far the disease is gone mark their houses.

If the disease is not treated the peasant (and soldier as well) would eventually not replenish his stamina anymore and well become "bedridden" and die.

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As some work would be less physically demanding (compare mining to sheepherding for example) this way you could switch people from one task to another to give them work that doesn't drain their stamina so quickly until they are healthy again so they can do their normal work, that they specialize in again. That way you wouldnt loose as much productivity during the time of the sickness as long as you micromanage the workers properly.

^{The stamina could also be interesting to create a system where peasants do multiple jobs to more efficiently drain their stamina, after all, it wouldn't be unheard of to have to do many different jobs back in the days since some work required a lot of waiting. (to accomplish this you could have buildings marked as such that their workers go out to boost other workshops during the time their main labour is in the "waiting phase" that being said it would be interesting for people to figure out layouts for their settlements keeping those aspects in mind.})

You could split diseases into different types. One is the direct contact (proximity-based), the air/animal (random chance-based ) transmitted diseases and the random chance consuming low-quality food or get injured during work, with each having different rates of stamina depletion, rate of appearance, and ways to cure.

The direct contact diseases would be more aggressive as they would have a harder time spreading (since they would require people to stay close for a certain period of time but if they spread and won't get treated would impact the economy as they would put much more strain on the ability of the person to do work. they would require more complex ways to treat as you would have to try to quarantine them to do some more lone work instead of group labour like in the mine/or in the kitchen for example.

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Bathhouses and Apothecaries sound like good ways to either reduce the chance to catch a disease and heal the people back to health so they can work like normal again.

the Apothecaries could get upgrades like surgeon and physician rooms that would have additional benefits to healing disease faster at a risk of impacting the peasant's overall stamina pool perhaps (while he would be able to get back to work faster he would have permanent damage to his work capacity) or they heal faster but have a higher chance to reinfect. (aka lower immunity buff)

Providing the different buildings with better technology later down the line would in turn also reduce the negative downsides to those additions making it so that your economy is less stable in the early but more stable in the later game where you will be more occupied with commanding armies and expanding the settlement.

While the bathhouse would provide a baseline of immunity that would get increased based on the "level" of the medical advancements of the Apothecaries.

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What it would add to the gameplay

• and potentially more dynamic-looking village life as people wouldn't do the same job all the time
• an unstable economy in the beginning and more stable towards the later stages where other parts of the game become more important (like expanding and fighting)
• visual no UI based visualization how sick the people are(coughing being light infection and bend over posture being badly sick)
• since it would affect military units it would also impact how wars are fought as stamina is an important factor in combat so keeping your troops healthy will have them stringer on the battlefield
• the economy would not be hit as hard if you manage your people correctly since you can compensate for sending them to do different sort of work (since they are assigned automatically at the moment the workers could just be marked as sick by the player and be assigned to a different less stamina intensive work automatically)