If we're comfortable letting a criminal go free of prison because guilt can't be proven beyond a reasonable doubt (and we should, for the record), we should be comfortable letting a child stay with its parents until the parents inability to care is established beyond a reasonable doubt.
The difference is that in one scenario it’s about punishing something that happened and is done and in the other it’s to prevent ongoing/future harm. If you’ve seen some of the things parents are willing to do to their own kids, you would see why it’s not that simple.