The idea is good, but it carries more then a bit of danger of becoming similar to the "cultural/ethic independent colonizing and migrating" thing in Master of Orion 3. Complex, well thought out, worthy of a masters degree and in the end very very difficult to control (therefore failing).
Any "autonomous spread" system would have to be tested to hell and back in order to reacb an acceptable level of ceertainty it wont break games here and there.
I would agree that any kind of channeler would have to have soem opportunity to combat disease if it does get in, because I can already see two or three tactics that would effectively render them severely hamstringed if they couldnt.
I agree it would be nice to diversify though. Just some thoughts (not thought thorugh very well , just something that would give each side its own feel)
Life - inocculate - channeler powers the spell and over a number of rounds infected people get less and less ill untill the disease dispappears (yep I stole that idea ^^ ), production incerases again as more people are once again fit to work.
Water - cleansing flush - immediate cleaned pop if acces to large bodies of fresh water. rest of the cities need to be supplied with the cure though caravans. (making them specialty caravans - player controlled)
Fire - healing fever - production drops significantly for a number of turns while the populations "sweats it out" If the disease has been around long enough some people might not be strong enough to survive the fever
Earth - Healing herbs - potions get concocted that will cure the disease and need to be transported to other cities without acces to...a swamp...forest....whatever.
Air - Benevolent breeze - stops the spreading of the disease immediately. People already infected will have to deal with it in a natural way (assuming less then 100% fatality here)
edit: for numerous typo's :/