It is much more realistic that what happened was a true "Burn after reading moment" https://www.youtube.com/watch?v=pabA320p9B0
He wrote about some of the things that happened in Geneva, I encourage you to read them. Even sysadmins for the CIA need to know some stuff about how the game works.
This feels like a strawman to cling to the idea that being a US citizen means that the CIA won't assassinate you for being inconvenient, which has been literally and directly claimed, at least twice, by someone from the actual CIA.
Indeed, the reason you even know the name Jason Bourne, or the reason those movies work, is because of the generation-long history and reputation of the US military intelligence services to break the law flagrantly in many countries with no meaningful consequences. We don't have to suspend disbelief to engage with the idea that there is a section of government with staff who can kill anyone they deem needs killing.
After CIA training, he worked in Geneva under diplomatic cover, in 2007 to 2009.