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.