See my child comment for a more in depth response, but to your point I believe it is naive to assume intelligence agencies would not weaponize something as powerful as a CP accusation.
In general or this case? In general: Because it's incredibly powerful. In this case? See below.
>The defendant broke his agreement with the CIA and the Federal Government by leaking classified information.
This has yet to be proven, and the defendant claims he is innocent. An alleged leaker claiming his innocence possessing unencrypted CP is incredibly convenient for the CIA. Almost too convenient.
>falsify evidence that could torpedo an entire case
Why when the risk to the gov is basically 0%. You run a kit to plant the files and metadata. The files are then "extracted" by a forensic tool, the "evidence" is now bulletproof. The only person who could conceivably challenge such a move would be a very wealthy person who knew they were innocent and chose to hire expert witnesses to analyze the planted data to prove it was faked. Even then... good luck.
I would think that just given time someone has falsified such a thing before, I don't by into the idea that it makes sense to make that assumption for any or every given case.
But a whistleblower? A thorn in the intelligence agencies' side who has exposed them and attracted their ire? You'd be a credulous fool to take that story at face value. The IC has a long and documented history of flouting norms like honesty and integrity. These are institutions whose entire purpose is to use deceptive, extra-legal methods to focus the power of government against anybody who poses a threat to it.