Just a few points about the use of the term "the government".
My basic understanding of the facts are that 1) McBride became aware of issues of crimes and suspected coverup and did report those through the CoC; 2) when nothing was done as a last resort he reported the matters to the media; 3) the Defence department reported the matter that confidential information was disclosed in these media reports to the Australian Federal Police and, after investigations charges were laid against both the journalist who received the documents and McBride; 4) the prosecution of the offences is in the hands of the Australian Commonwealth Director of Public Prosecutions; and 5) the CDPP has previously dropped charges against the journalist.
You should note that, like her Canadian DPP counterpart:
So the fact of the matter is that the "government", per se, is not involved in either instructing that charges be laid or interfering in the case. It's all to easy to use the term "the government" to create the illusion that some central authority is pulling the strings but, while one can have suspicions, the facts of the matter are much more innocent.
In many cases where a federal crime is alleged to have been committed by a federal servant it is quite normal for the department involved to provide the information/evidence respecting the crime to the federal police services who will investigate the offence, consult with the prosecutors from the DPP's office and, if warranted, lay an information or charges with the DPP whose office will then prosecute it in a federal court. It never involves any element of the government's executive branch which would be both improper and unusual.
Obviously all of our senses are heightened about our own recent experiences with Adm Norman but that case touched on cabinet secrets which obviously fell much closer to the line of the executive (and perhaps actual interference or animus) which is not present in the McBride case.
Based on McBride's own admissions, he clearly broke the law. The question that is left is: was he justified in doing so to the point that charges should be stayed or withdrawn. All that I know is that he tried to work through the CoC before going public but do not know to what extent he may have tried to "blow the whistle" let's say to their Defence Minister. The Inquiry's report seems to say that the "coverups" were fairly low level. It would be very interesting to see details on what levels McBride's internal complaints went to and why they resulted in no further action. I presume that's included in the censored portion of the report.
Like you, I distinguish between the technical guilt of having done the crime in this case with the moral necessity of bringing to light significant wrongdoings. I too feel that it would be in the best interest of justice to have the charges stayed. That, however, is the role and decision of the independent CDPP. It would be as wrong for "the government" to pressure her into withdrawing the charges as it would have been for them to urge prosecution.