[Edi]

Mabakiel, Pazuzu, Harvester of Sorrows, Poison Golem, Bane Venom Charm, all of those spread disease that way.

I think there is also a disease spell that kills population (Black Death or something), so someone could be hammering you with that. If you have domes up and they are still standing, then it's something from the first list. Either summoned by the enemy or summoned by you, it doesn't discriminate.