That is interesting that your daughter was suspected to have tongue thrusting - that's what my doctors said at first, too! Checking hormones is a good idea - thyroid can cause issues like this. My thyroid was negative though (It's usually part of the blood tests, so if you received copies of the results, you might want to check it out!)
As for doctors: my uncle is my dentist, so he noticed the resorption first through my x-rays. He went to the University of Michigan, and is friends with the retired chair of oral/facial surgery there, Dr. Norman Betts. My uncle referred me to Dr. Betts because he is supposed to be the best for such rare conditions. When I met with him, Dr. Betts refused to do any surgery (it's an invasive procedure involving condylar reconstruction) until the cause of the resorption was diagnosed and was in remission. Dr. Betts stressed that condylar resorption is a *symptom* not a diagnosis. That is when he referred me to Dr. Hilary Haftel, a rhumatologist at the University of Michigan Hospital, even though I explained to him that other doctors had concluded I had no autoimmune disease via a series of negative tests. I ended up meeting with Dr. Haftel anyway because it was convenient for me, as I am a graduate student in Social Work at the University of Michigan. Dr. Haftel is an absolute expert in rhumatology - the best - she also teaches at the university. (Fun Fact: Michigan is where "House" went in the tv show "House." Haha, I guess that gives it a good reputation, sort of.)
Anyway, this is the confusing part for me - there was no evidence whatsoever that I had an autoimmune disease even after Dr. Haftel's tests. There are only a few ways to test this, and none of them have to come out positive for a diagnosis. Tests are: blood work, the doctor checking for nodules, swelling or redness on/around the joint, and finally a contrast MRI to check for any "active processes" like rhumatoid arthritis. In my case - all three of these came back negative. Blood was fine (no Rhumatoid factor), no swelling or nodules and even the MRI did not indicate an active process. However, for me, there is no joint left - at all. I no longer have condylars on either side, so there would be almost no joint to examine anymore. After Dr. Haftel read the MRI she concluded that the bone loss was consistent with JRA...despite my complete lack of other symptoms.
Or at least, I thought a complete lack of symptoms. My mother has since convinced me otherwise...as a child my growing pains were way more severe than normal (e.g. I actually complained, where most kids don't.) and my jaw ever really hurt...more than an annoying toothache feeling. However, JRA can inflame tendons around the joints. I did notice the tendon issue; I was a dancer and some days my knees and arms would just hurt. (But, never in *that* noticeable of a way.) Now, I can notice it...but the pain hasn't been that bad, which apparently is very rare - usually it really hurts, according to other people with JRA or autoimmune diagnoses.
I find the birth control bit VERY interesting. This bone resorption didn't happen to me before I was on Depo Provera (the shot)...it happened during and after I stopped taking the shot. There might be a connection there - but, Dr. Haftel didn't seem to think so.
Anyway, I also really like taking the holistic method as well...however, because this may be a serious condition (I mean, if it happened to one joint...what's stopping the other joints from disappearing later?) That's not meant to be scary...it's just how I'm kind of feeling about it. I would really, really recommend getting a diagnosis...bones don't absorb into themselves and disappear for no reason. (Note! I also used to go to a naturalistic chiropractor for scoliosis as a kid - apparently if your daughter does have an autoimmune problem, lubricating the joint via 'cracking' can irritate this problem.)
Anyway, I would recommend looking into Dr. Hilary Haftel at the University of Michigan in Ann Arbor. Also, on the 'hypermobile' joints - I also have heard that in the past. My elbows over-extend to the point of looking almost broken! However, I talked to Dr. Haftel about it and she said that no matter what, a joint is a joint - and no amount of hyperextension should wear it away, in the way mine wore away. She said it might explain slight bone loss through 'wear and tear' but, nothing like this complete condylar resorption. I guess it depends on how severe your daughters loss is. My open bite was only 1mm for a long time...two years later it became over 3mm wide. My teeth do not close together in the front at all, and the whole shape of my face has changed. (Slight chin recession, shorter forehead to chin distance)
If you or your daughter ever want to talk - feel free to write me. This is a very annoying and scary process. When I was 17, it really irritated me because I just wanted to go to college and not care about it - which was easy for me to do because the resorption is so slow moving and random. Anyway, feel free to contact me if you want. (My real name is Kathryn.)