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.
So what is the relative frequency of these two outcomes? You can't ignore the wrong applications; if they outnumber the proper ones, then the system is doing more harm than good.
So, in this particular case, I would say that the justice system did it's job quite well, and it's a massive failure of the medical system that shaken baby syndrome is still identified as a real thing by real, board-certified doctors.