I have a suggestion; not sure if it's doable, but I'll throw it out there. Give a building (maybe Granary?) the following trait :
For every
two farms with
fresh water, and for every
three farms with
no fresh water within
3 tiles of a city, gain +1
in city
.
And have the food bonus either scale with era or improve with later techs and/or buildings. This should mitigate the balance discrepancy of getting a start with fresh water vs getting a start without, as if you start without fresh water access for your farms, you can still potentially keep up with Civs who do have fresh water starts, but you must necessarily prioritize and invest more heavily in your agricultural infrastructure, which makes complete logical sense. This also acts as an indirect buff to farms, since the bonus will apply regardless of whether or not the farms are actively worked by the city populous, and thus encourages players to plan out the ratio of farms to forests/jungles.