Are there in fact any fatal flaws in the military/civilian organization of NDHQ?
The one that most people zero in on, is the occupation of the same organizational box by the CDS and the DM, with the two of them being co-equal and being co-chairmen of various groups. That allows both military and civilians to work together, while maintaining the differences in conditions of service, which are vast, between the two groups. (For example, broadly, the civilian owns his job, while the service person owns hs rank.) In consequence, different expertise can be brought to bear on problems.
The other flaw suggested is that association with civilians somehow reduces the "militariness" of Service officers, and that they tend to manage rather than lead. In the author's opinion, the top leaders of the Armed forces need to be able to bring a wide range of skills to bear to be able to function; such leaders have to have both the skills of command and the skills of operating in the complex atmosphere of any national headquarters.
On one hand, the basic NDHQ set up has achieved a great record of success for nearly a generation. It is by no means a perfect organization, but it does work. The notion of "pure" military decisions has perhaps never existed in this country, and certainly has not for at least 75 years. It follows that better results are likely to be achieved by civilians and Service people mucking in together, than by trying to deal at arms length.
On the other hand, it requires great tolerance for the existing organization to function, and we are talking about great tolerance among strong minded individuals. The incumbents of those two positions must be prepared to accept joint accountability for their decisions.
On balance it is fruitless to waste time on the impossible task of devising a perfect organization for Canadian Defence, and put that effort into ensuring that whatever organization is in place, does function effectively.
In a word, anyone who thinks the problems of the Armed Forces would be solved by changing or disentangling NDHQ is dreaming in colour.