The reason to not destroy everything when you pick up the factory is so that you can move them. Which, IMHO is a good thing.
I would instead recommend a new item to "clear" a factory, destroying everything inside as well as the surface, and also verifying that the surface is created on fist entrance (not on placement)
NOTE: this response is mainly meant for the Mod Dev, and not the OP specifically. Though this might explain to the OP why it is the way it is.