In the official friendship is magic comic (Fiendship is Magic #5) they explain that she was born from a carnivorous tree. The tree was planted in a magic pond that began to devour insects and the bones of ponies that died in the pond. The inside of the plant, with the help of the pond, the insects and the bones merged together to form the changelings and Chrysalis.



So part of your theory is right about a radioactive environment.