The essence of the decision on the constitutionality is at paragraphs 28 to 33. In short, prosecutorial independence is a principle of fundamental justice. And yes, the Minister of National Defence - like his Cabinet colleague the Attorney General - plays a political role. But it does not make him or her as violating the principle of prosecutorial independence per se. Actually, there is "a strong presumption that he exercises prosecutorial discretion independently of partisan concerns" (para. 32). Unless there is clear evidence that the Minister acts on illegitimate political motives - which would constitute an abuse of process (see R. v. Power,  1 S.C.R. 601, p. 612‑615; R. v. O’Connor,  4 S.C.R. 411, p. 465-468) - courts must not intervene in the prosecutorial discretion.
This is an interesting decision in that the court does not seem to have regarded the position of the Minister, as the epitome of the chain of command from which prosecutorial decision making should be independent, as a material consideration. In the UK Service Justice System, section 34 of the Court Martial (Appeals) Act 1968 and Rule 51 of the Court Martial Appeal Court Rules 2009 permit a reference to the Court Martial Appeal Court by the Criminal Cases Review Commission, or the Judge Advocate General or the Secretary of State for Defence. So, the anomaly exists that an independent prosecuting authority is unable to refer a matter, even via the Attorney General, for clarification of a point of law, yet the Secretary of State for Defence, from whom the Director SPA is independent, can. It is difficult to understand what prosecutorial function the Secretary of State for Defence/Minister carries out, in regard to the Service justice system. It therefore strikes one as a true anomaly that there is any right for that governnment official to enter an appeal. The Attorney, on the other hand, is a law officer and, in the case of the UK SJS, has a supervisory role in relation to prosecution decisions. The Secretary of State, or his/her ministers, do not. I may be wrong (as I am not as familiar with the Canadian system as I would like to be), but I do not see what prosecution function, within the CF justice system, the Minister has, if Prosecution decisions are taken independently by legal officers. So, it seems to me that s.230.1 NDA specifically breaches the independence of the prosecution function by giving a prosecution right of appeal to the executive from which it is supposed to be independent. The same goes for section 34 of the Court Martial (Appeals) Act 1968 and Rule 51 of the Court Martial Appeal Court Rules 2009.
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