You can also avoid it to some degree by controlling squalor and building health bonus buildings. If your governor has a doctor etc you can have health bonuses. There are also traits which give health bonuses IIRC.

Best thing to do now is like I said, get them out of the affected settlements and SIT them somewhere. They may survive, I know lots of mine have.

Prevention is better though, build larger walls, increase tax rates and control population growth best you can.