The long-con theory seems a bit more plausible at the moment
To me that's way more plausible than losing control of your account and the person who compromised it then having someone over a long time insert the backdoor that took a long time to develop and then obfuscate it.
Likely someone at GH is talking to some government agencies right now about the behavior of the private repos of that user and their associated users.
I would not be surprised if there was a group using this approach, but I doubt most of them are/would. If they were that dedicated, they'd just have a fucking job, instead of being dicks on the internet for a living.
With the added bonus that sometimes they get to pull off a longcon like this.
So most likely he didn't wait two years to benefit.
Or they WERE legit and simply went rogue, perhaps due to external factors.