This sounds very much like presumed guilt rather than presumed innocence.
Judges can issue preliminary injunctions before trial in all places in the world. A justice system that can't take any coercive action until the end of a trial would simply not function.
In particular though, cases like this aren't even related to the presumption of innocence. The state believes that the child has suffered harm, so a judge takes them in protective custody. Who is harming the child remains to be determined, but taking the child into custody is supposed to protect the child immediately.
Of course, this can be, like in this case, wrongly applied to disastrous effects. But it has also saved many children from abusive parents, where leaving them without state protection for years while the trial advances would have scarred them permanently or killed them.