I disagree with most of your points but let's take an example of how TV/propaganda differs from reality: On TV, brave agents would be "incapable of any sort of undercover/sting operation." In reality, a super-leak would end abusive and dangerous confidential informant ops that depend on blackmailing CIs into enticing others into pseudo-crimes. CIs also commit thousands of crimes that they get away with while being CIs. The FBI wastes a good deal of time on these ops, which might have something to do with why, after his co-workers had concrete concerns about the Orlando shooter, the FBI found nothing wrong. Secrecy hides a lot of ineffective, expensive, and abusive practices.

In every area you cite, it is likely that secrecy hides more appalling counterproductive corrupt practices than it protects secrets that make us safer.