The root issue isn't that it's the military is in charge of these departments, but that people who aren't qualified and experienced are heading them up. So, in most cases, the generals or other officers who get parachuted into leading orgs aren't familiar with the org's work, culture, team, or vision. In the best-case scenario, they come in, sit and watch, and in the worst-case scenario they drive the real talent out of the org and, eventually, the country.
The problem with Pakistani generals is that they have a real bad case of 'desi uncle-messiah syndrome.' They can't and won't delegate to others. Despite the fact that there are millions of civilian Pakistani experts in a huge range of fields (a big % being of military lineage), generals will not lean on them and will insist to manage these orgs themselves.
This tells me that it isn't 'privilege' or 'discrimination' driving the thought of our generals. If it was only discrimination, then at least civilians who are the children of retired officers would be asked to lead said orgs. But we don't even get that. What's driving our generals' thinking is just some irrational mental block. It's just stupidity.
Actually you started your post with exactly the right idea. The problem is that UNQUALIFIED and INCOMPETENT military people are heading organizations or put in leadership roles. And the problem with them is that they are extremely threatened by anyone with talent/ideas. Case in point what happened to the head of Azm - a PAF guy, who with his faults was a technically competent person, and was moved to an administrative job by superiors that felt threatened, and then left the service. You're right that it's not discrimination - that wouldn't explain it. It's insecurity.
Also I think we've derailed the thread lol.
I think PAF is not doing anything official because of the generally negative perception of the armed forces these days and the bad economy. I mean, as long as they are building capability, who care if there's a reveal ceremony or not. Clearly, work is being done.