I've given some thought to disease as well. I would keep religion and instead add disease as something that is similar but distinct. The 7 diseases that I came up with are:
* Bubonic plague
* Cholera
* Smallpox
* Influenza
* Tuberculosis
* Measles
* Typhoid
Instead of being tied to particular technologies, I envisioned these as being found in various geographical locations. A disease would spread along trade routes. In addition, your units could be infected with the disease. If you had partial immunity, that would make them carriers. Carriers have a chance of spreading the disease to units and cities on the same tile. Any unit could thus be a disease "missionary."
Over time, individual pop heads and units would build up an immunity to each of the diseases, so getting exposed early means you hurt early but build up your immunity sooner. I would raise the default health bonuses on each level to compensate for the introduction of disease. Certain technologies would diminish their contagiousness and fatality rate, while increases to health would happen as in the standard game, but the only way to eliminate unhealth caused by disease would be to become immune.
When a disease spreads to a city, it would add to its unhealthiness immediately, with that boost diminishing slowly over time based on immunity and the other factors mentioned above. The same would happen to when a unit is infected. Its strength would be greatly affected, and the unit could in fact be destroyed outright. Note also that the chance of a disease spreading to uninfected cities and units on the same tile increases with more units on the tile. Thus, you wouldn't want sick units to mingle with healthy units, or Typhoid units to mix with Flu units. Stacks would be dangerous.
* Bubonic plague
* Cholera
* Smallpox
* Influenza
* Tuberculosis
* Measles
* Typhoid
Instead of being tied to particular technologies, I envisioned these as being found in various geographical locations. A disease would spread along trade routes. In addition, your units could be infected with the disease. If you had partial immunity, that would make them carriers. Carriers have a chance of spreading the disease to units and cities on the same tile. Any unit could thus be a disease "missionary."
Over time, individual pop heads and units would build up an immunity to each of the diseases, so getting exposed early means you hurt early but build up your immunity sooner. I would raise the default health bonuses on each level to compensate for the introduction of disease. Certain technologies would diminish their contagiousness and fatality rate, while increases to health would happen as in the standard game, but the only way to eliminate unhealth caused by disease would be to become immune.
When a disease spreads to a city, it would add to its unhealthiness immediately, with that boost diminishing slowly over time based on immunity and the other factors mentioned above. The same would happen to when a unit is infected. Its strength would be greatly affected, and the unit could in fact be destroyed outright. Note also that the chance of a disease spreading to uninfected cities and units on the same tile increases with more units on the tile. Thus, you wouldn't want sick units to mingle with healthy units, or Typhoid units to mix with Flu units. Stacks would be dangerous.
I don't really have the technical acumen, which is why I suggested a simpler model. Even in order to make the simplest disease mod I would have to go through the files and figure a whole lot of stuff out, mostly through trial and error. I've been teaching myself scripting languages to fiddle with games since I first learned to type (probably 11 yrs ago), but I'm not superman, unless superman can't fly any faster than a snail's pace. 
