Might the solution be an independent agency which centralises whistleblowing? Whose decisions are appealable to the courts and legally required to balance public interest and national security?
I can't speak for the rest of the government, but I can speak for internal whistleblowing of the Marine Corps. You can "request mast" all the way up to the Commandant, which is the tippy top. I think it's possible that some whistleblowing is discarded when it should have been honored, but I think for the most part these processes exist and are in-tact. Now, whether there's a perception that you can use them effectively is another issue.
Let's not forget someone whistleblew on the President amid a highly political environment in recent memory. That's no short order.
There is no recognized public right to know any information that subverts the defense apparatus or benefits a foreign adversary. So even if you want to reveal a war crime you may need to wait until after it can't be proven in court to jeopardize national security. Until such time you would need to limit your disclosure to approved channels.
Anything else is treated differently. Stuff like waste, abuse, environmental issues, discrimination and the like are usually a different ballgame.
Except that, "national security" has grown into an all encomoassing concern for juat this reason. It can be used to hide thay which is condemnable or embarassing.
