The reason it is set up how it is, is to protect the innocent. The principle is that it is better to have some guilty go free than even a single innocent locked up.
I understand and am fine with the presumption of innocence I am just not so comfortable with the assumption that just because you are found by a Judge, Magistrate or Jury to be ‘Not Guilty’ it doesn’t automatically follow you didn’t commit the crime, rather in some circumstances based on all the available evidence there may be grounds for an alternative verdict of ‘Not Proven’. There is a distinct not so subtle difference.