Purely brainstorming here:
Maybe a bit of both? If settlements aren't properly dealing with their dead I imagine disease will be their reward. Same with sieges. That forces the player base to deal with the deceased rather than leaving corpses strewn everywhere. (Hopefully we can still use treated bodies as war trophies, such as heads on pikes etc)
Perhaps upon discovering a new continent there'll be deadly diseases exchanged, look at how devastating European disease was on the natives in the New World.
Whether mann can make plagues, that seems unlikely. Perhaps disease could be strengthened somehow though. So say a disease gets stronger the longer it survives, by collecting and controlling it among livestock it could be brought to biological warfare/terrorist levels of effectiveness?