I remember reading a thread a short while ago that suggested putting the units (if you can spare them) on board a ship.

I tried this, and I kept getting a plague msg with no soldiers killed, until my 10 star general died. But, when a few turns later I conquered Corinth with this army (after having no msgs about plague etc) Corinth instantly had a plague... I need to test this more. Has anyone used the ship method and had the plague actually go away from their units, or are they just in some sort of stasis while they are aboard ships?