Thanks for bumping this up, I would've nearly forgot to post in here. I think the less you hear about D-9341, the better, because it's easier to associate with someone you hardly know about their past rather than one that isn't at all close to one you would experience. I think the 'wrongly accused' story could be interesting though, I don't exactly know, as you said, how it could be proven it wasn't you.
But my main idea here is a bit more of a extension on a current plot-line: 079. It appears somewhere between an antagonist and a acquaintance in this story, it seems vaguely out of character to me, because he is so simply underused. His intentions aren't very clear, it can be argued that he just needs your help, but I feel he most definitely has ulterior motives and shouldn't be trusted entirely. He just asks for you to turn the remote door control back on... and you do and he opens Gate B. The end.
I feel he should make some other appearance though. Possibly in the ending, maybe just randomly scripted sequence.
I think for a scripted sequence, a randomly playing glitch-like sound emitted over the PA by 079 accompanied with the doors around the player opening and closing suddenly. I feel it'd be rather ominous and possibly disturbing, taking after GlaDOS in the first Portal.
http://www.youtube.com/watch?v=ruT7N1LRaBA
It slep time bunner.