Salary is just one thing. There are other factors such as lifestyle, nature of job, potential for growth, etc.

As a civil servant, along with the salary, you have more influence (at least PAS/PSP/PCS). You deal with the public directly so over time, you end up having good PRs with a lot of people. The downside is, your job is way harder compared to the strategic orgs.

Growth is one of the key differences between the two. While the growth in civil services is pretty much endless (you can go all the way up to secretary/IG), but strategic orgs such as SPD/NESCOM are dominated by the military. The potential for growth for civilians is not as high as for uniformed personnel.

Civil servants enjoy protocol and vehicles (if that's your thing), a BPS17 (or SPS 09) officer doesn't get any of that. As opposed to an civil servants, employees of the strategic organizations are actually discouraged to disclose who their employer is, where their office is, what they do, etc. The upside is, you don't have to deal with public or get up at 2am because there has been some incident in your tehsil. Downside: not as many PR as civil servants, obviously.

In my opinion, each has its own pros and cons. It all depends on what you prefer.