First, we all have religious freedom to think whatever it is we want to think, and to organize our religions. But this freedom does not translate to all religious actions, if they are actions that break state or federal laws. The Zion children are not in protective services because the State doesn't like the way the women dress, or anything like that. The children are in the custody of the State because the minor girls are pregnant. DNA tests are being run to help sort out what is going on.
Second, we have agreed as a community to protect our children from abuse. We have established services in our States which look out for those interests. In the case of the Zion Ranch, the children have been put into protective custody of the State of Texas because there was enough compelling evidence brought forth at the initial trial that the children living in this compound are at risk of abuse.
Will the children stay in State custody? We won't know the answer to this until the investigations are finished, and the court proceedings continue.