The Doctor was able to use his sonic screwdriver to stop the upload. Since the sonic screwdriver is Gallifreyan technology, and has a psychic interface, it would have been far better at reversing the download than Clara's comparatively primitive early 21st century human netbook, if only because it would let the Doctor hack that much quicker.
The plot of this episode foreshadows the Myth Arc of Series 8. Given that, it is entirely likely that Missy was quite pleased that the Doctor and Clara had taken care of her competition for Human Resources for her, don't you think?
