I recall there used to be an Earth spell to revive land, but I haven't played up Earth lately enough to see if it still exists.
Revive the Land still exists, but moved from Earth Magic to the Magic Research tree (I believe it's under Rituals or Sorcery, but I could easily be mistaken). I don't recall if it can target city tiles, though, and I don't believe that it's guaranteed to produce a tile you can settle on. Note that Revive the Land is the Kingdom version of the spell; if you're playing an Empire, you want Bloom of Twilight.
But so I guess it's old news that there's this feature that razing a city seems to permanently destroy the fertility of the city tile and its surrounding tiles
While not ideal, you can change this by modding the tile type left behind after razing a city to have certain food, material, and essence values. I don't know what you'd need to change off the top of my head, though asking around in the modding subforum will probably get you a solution fairly quickly.