[Uh-Nu-Buh]

I think a few positive-effect magic sites would make everyone happy. Make them even rarer than the death/disease sites. Maybe only one of each in any one game.

Great Life Garden: Nature gems, cures diseases.
Sparkling Spring: Nature gems, heals afflictions.
Soaring Falls Shrine: Nature/Air gems, increases population rate.
Ancient Earth Temple: earth gems, removes curses.

People would have to go on quests to get cured. The diseases, curses, afflictions would all still have a large effect on the game--units would be taken out of play for a time. Probably only heores, commanders, and pretenders would make the pilgrimage--and while they were journeying they would not be fighting, spelling, or otherwise having an effect on the game.

Those provinces with these sites would be some of the most valuable in the game. Fiercely contested over, just like fortresses.