I don't see the question here as having to do with the government telling people what their religious beliefs should be, but rather at what point in life a minor can reasonably be allowed some say in the matter. I see that as a common undercurrent in both cases. The Stanleys are claiming that the removal stems from the desire of their teenagers to go to public school--which would violate the parents' strongly held religious convictions. Now, possibly the conflict led the teens to tell on their folks who were already regularly engaging in dangerous practices (whipping children into submission, or dosing them with MMS), or alternately their "rebelliousness" (in quotes here because I see that term being reiterated in fundamentalist literature vis a vis children besieged by the spirit of the devil--and must be "chastened") has led to chastening at a level that actually crosses the line into physical abuse.
Now, in the Bary case, it is unclear exactly what the Bary's knew about their daughter's conversion, nor the extent to which she was attending various campus ministry events (which actually ought to be a concern for the parents of any high school girl--regardless of any religious intent to the activities). It was clear however that there was friction between the family and their daughter from time to time with regards to the practice of wearing hijab when she might be seen by friends (on the way to mosque), as well as her developing online friendships--which led to the incident of the father raising the laptop up as if to strike her. Beyond that there was a good bit of anti-Muslim invention about threats of honor killing (a cultural practice not found in Sri Lanka, the family's country of origin--not to mention not typically a response to religious conversion) and preferential treatment given to Muslim families over that accorded to Christian families by Childrens' Services.
But, again--the question remains the same. And the objection to the UN Statement of the Rights of the Child which you raise centers directly on the rights of children, at some "age of reason" to be allowed a choice in the matter.