Fathers who molest their kids are not reunified - if that happens, it's because the allegations were not supported.
Abuse is not just extreme abuse involving poisoning and rape. It used to be, but after a lot of outcry due to children dying from more neglectful situations than actively abusive ones, social services got a lot more involved. That now encompasses failure to get them appropriate medical care in many situations, as judged by doctors. It can be a fine line, obviously.
I don't think Children's believes the Tufts doctor was inappropriate - that's the piece people seem to be missing. If they believed he was subjecting her to insane, unsubstantiated treatments, he'd be in trouble. What exactly was he doing for her? It seems like treatment for mito basically involves vitamins and rest. If in his opinion that seemed to explain the symptoms, and he monitored her for that and gave recommendations on how to stabilize and some meds to address the symptoms, and referred her to other specialists for some of the problems, he was doing his job perfectly fine. It's not a diagnosable condition - it's a matter of judgment, and he may have been making all the right calls.
I do think that when Children's saw her, something was a big red flag, and that's why she has been in psychiatric care so long. Once they started evaluating her mental state, they got more and more concerned and reported it. Maybe they thought the parents were lying to the doctor and exaggerating symptoms, or asking for too much medication. Maybe they thought the doctor's treatment was fine for some of her symptoms, but that the parents had neglected to address serious mental health issues that were posing a danger to her that should have been taken into account. Maybe they had prescriptions from other doctors. Who knows? But the abuse was definitely not thinking she had mito and treating her for it - that is 100% not abuse. We don't know the details, but if it were severely abusive, they wouldn't be trying to reunite her at some point, and they'd be facing charges. It sounds more like non-criminal neglect - like the parents may truly believe she does not have mental health issues and want to treat her only for mito - that's all legal conduct. But if social services thinks she is in danger because the parents are difficult and stuck to their beliefs even when she needs serious help, they will take her away for neglecting to get her the mental help they think she needs. That's the issue here - not their belief or what they've done in the past. It's going forward, will they agree to get her the psychiatric help the authorities have agreed she needs. If they do, they will get her back. If not, they can't let someone unstable out into that environment, even if everything the parents did was legal.