Can ingesting substances that are produced by the body cause a permanent withering of the organs that produce the substance?
Yes it is possible but in most cases it will not occur as the body simply halts production. The most infamous manifestation of this is in adrenal insufficiency. That's where when we take glucocorticoids (e.g. prednisolone used in management of lots of inflammatory diseases like asthma and autoimmune diseases) for a prolonged period at high dose. This causes the adrenal glands to atrophy (physically shrink) and following this sudden withdrawal can be dangerous for a patient. That's why we always slowly withdraw steroids when a patient has been on them for a long period of time.