Unless I completely missed something (which is possible), my recollection is that in my two recent Scion games my cities had zero unhealthiness from the very beginning.
I know/remember that one of the Scion UBs (the Necropolis, I think), gives hammers based on life mana and other "health" resources such as corn, rice, wheat (but not any of the seafood health resources, I don't think). This shows up in the city screen as a "building" called something like "Harvested Life Resources."
The last time I played (whenever that was), the Scions get a penalty to happiness/productivity when a city is unhealthy, but the Necropolis from the Necromancy tech removes unhealthiness from population for them, effectively negating the issue.
plus GP points, and there are some events that occur if you have a Mage Guild, but still, doesn't seem quite right, I don't know.

(ok, i forgot about chariots, but hey, they don't use much different weapons than regular horsemen)