Diseases still exist. In a matter of minutes, 4 of my villagers contracted the plague. My guess is an imbalanced diet led to it since the start up homes are in an area that only gets fish and the starting bread in it,while the outer lying new houses get a more balance fruit, vegetable, and meat diet.
If I'm right the problem is primarily due to the starting position and limited development directions which lead to the lop sided barn inventories. A "warehouse manager" or some such individual could be charged with keeping the inventory of barns balanced or a market that pulls stock from each of the barns for population use. Better starting positions that don't cram you into a small area would be a long term solution (or provide nothing but a barn and warehouse that are automatically placed, built and stocked where the player wants them.)