Things are not as clear as you would like to believe. There obviously is evidence that Justina Pelletier has been medically abused or neglected by her parents. With no evidence, they would not have been reported multiple times by medical providers to DCF. With no evidence, the judge would not have ruled multiple times that Justina's Parents were not fit to care for her medical needs. With no evidence, the guardian ad litem would not have recommended that Justina NOT be returned to her parents' custody. Evidence of abuse or neglect has been presented (multiple times at this point) in court. Since the court records are sealed and the professionals are prohibited from releasing medical information about Justina, the only information you are reading is coming from the parents directly or from a small amount of leaked documents. It is in the parents' best interest to continue to claim that no evidence has been presented. Considering the circumstances and events, that is simply not possible.
You are assuming that the parents were following a Tufts' "protocol for treatment." The parents have claimed repeatedly and loudly that they "only wanted to follow the Tufts physicians' medical instructions." Considering the fact that the Tufts medical staff had previously filed a report with DCF alleging medical abuse or neglect, that claim does not exactly ring true. The Pelletier's have shown considerable evidence that they want to be able to pick and choose which diagnosis to embrace and which treatment to provide to their minor child. That would be fine if Justina did not have significant medical needs. It is not fine, and therefor it is neglect, if they are choosing to ignore and refusing to treat a life threatening or emotionally damaging diagnosis. Obviously, the judge believes that the evidence indicates medical abuse or neglect.
You are also making some assumptions about the Tufts Medical Plan that you can not possibly be privy to - mainly because the Pelletier family has said as recently as today that they have not yet met with the Tufts doctors and therefore do not know the details of the Tufts Medical Center medical care plan. As stated on the Miracle for Justina Facebook page "...still waiting on the tufts meeting!!" It is very possible and imo highly probable that the Tufts plan (which would be newly developed after Justina's recent appointments and evaluations there) will contain much more then "treat for Mito using exactly the plan favored by the parents." The Tufts plan may or may not confirm a Mito diagnosis - after all, Dr Korson has been quoted as stating that Justina had "Suspected Mitochondrial Disease." In medical-ese, that indicates an unconfirmed possible diagnosis. The plan likely calls for continued psychological counseling since Tufts was recommending psychological counseling prior to Justina's admission to Boston Children's. The plan may very well mirror the Boston Children's Hospital care plan that the Pelletier parents vehemently objected to. We will know that to be the case if the parents start claiming that the doctors at Tufts were influenced by, intimidated by, or bullied by Harvard/BCH/ECF etc.