Just thowing an idea out there, what if instead of having the shard automatically change types, what if it required a corruption/purification spell.
That spell could have a range of 0 (with allowance made for a shard that's integrated into a city), and could require the caster to hold a particular consumable component. In addition, the shard type could dictate the type of surrounding land (let's say a 6 square radius?), such that even if empire took over the nearby city, the land shared by the light shard and the city would be fertile. I assume terrain penalties for fertile/corrupt land still apply to the units of empire/kingdom factions?
Maybe apply food penalties/bonuses for city buildings that are in the radius of a shard, depending on if the shard is the appropriate faction.
And maybe Ceresa's existing shard corruption spell would forego the need for her to have the consumable component... although there might be some balance issues there depending on how difficult that component was to come by.