I wonder if you could use in-game mechanics to expire these entities and avoid having to do anything with control.lua.

EG captured biter nests convert to normal nests after a period of time.
In space-age\prototypes\entity\entities.lua .. look for "captive-biter-spawner".

Its a machine that if idle slowly loses health. Your entities could be something similar that leaves nothing behind.

Today I found production_health_effect—my bad. So yes, it is possible. It could be done without Space Age, but everyone would need to agree on the same prototype value: the time until it is destroyed. I'll try to implement this as a mod setting, but no promises.