When the Americans play hardball, Samsung should be prepared but it seems like they caught them completely off guard.
By now, I'd be surprised if they were even able to isolate where in their production line they were sabotaged. I'm guessing they introduced multiple points of failure and also introduced some security bugs into Android to target various components.
When dealing as a major global corporation, and especially if your main competitors and antagonists are the likes of American corporations, being prepared for sabotage by CIA etc should be part of daily ops.