That justice system you mentioned is just designed and founded to whitewash Israeli warcrimes and IDF's crimes against humanity to reduce the reactions from the world. If you consider the main purpose of the system, it's obvious that it was a marvelously operating until Operation Cast Lead. It was too unfortunate that we had chance to see some of the warcrimes like using phosphorous sheels on civilians. The only problem of IDF's law enforcement is now that the world has an idea on how many cases should be brought to court is known by the world and the cases brought to court just doesn't match it.
US rally shows support for ex-Marine held by Iran on spying charges (AP)
from the article: IDF's law enforcement is a joke of a justice system