[off topic] There was a comic where someone slips Clark Kent information about an illegal plant dumping chemicals. He shows up as Superman and stops the crime, but the whistleblower is angry that Kent informed Superman instead of digging up the names of the real owners.
Hell the CIA had enough trouble trying to kill Castro, exploding cigars etc, etc etc, that this would almost write itself. And since they were so bad at killing a normal human I doubt they would ever get suspicious that Clarke manages to avoid every trap they set for him.
One scene could be where they're in the office and the facial recognition software keeps trying to identify Clark Kent as Superman, but they just can't believe it, and one guy says "That's not Superman just look at him. This guy wears glasses!".
Edit: In case anyone out there reading this is actually from the CIA, we're just kidding guys/gals, we believe in you.
This is the first pitch on Reddit or Lemmy in 12 years that is actually good and doable and interesting. Make Lex Luthor one of the assassins in his early days... Yada yada yada
I'm kinda wondering if this would actually work with the audience who knows Superman's lore. It'd be like watching an episode of Blues Clues. "Gee, I can't seem to figure out why those nineteen whole bullets that absolutely hit him square in the chest didn't even slightly kill the guy." "HE'S SUPERMAN YOU CONSUMMATE DINK!"
I mean MAwS is basically this from the other direction, Task Force X is assembled with the intention of tracking kryptonians specifically, and Clark gets sucked into that without them knowing he even has a secret identity they could use to figure his deal out.
Metropolis is in the United States & Clark Kent is a US citizen, therefore the CIA cannot touch him. They just informally encourage the FBI to keep an eye on him.