I really enjoyed this story. It had all of the elements of interesting Sci Fi and the interesting post-singularity issues were developed and presented nicely. What bothered me about this story and stories with similar endings is that I don't understand why a choice was necessary. She was digital. There's no reason why one digital stream couldn't be sent to that underground repository while an identical digital stream was sent off to create morality for a new generation of digital consciousnesses. When you're digital, you can have your cake and eat it, too, although you may not be able to taste it.
Therein lies the rub, really. The story made ostensibly about a post-human conciousness running on a server, but it really treated her mind more like a soul; not only could she not have multiple copies existing at the same time, there was a strong sense of continuity between her different iterations. In reality, if the government controlled her servers they don't need to delete anything from her memories - why not just reset her to a backup state?
Not that any of that detracted from my enjoyment of the story, mind you. Taken as a story, it was really, really great. It's just that I think that in addition to the philosophical implications it was intended to raise, it has a whole set of unintended ones that probably nullify a serious discussion of the first.