Second, the question isn't necessarily whether the initial transformation wiped out humanity: the point is that the transformation would render the Earth completely uninhabitable. Remember that at that point, nobody had developed working Tiberium Infusions to immunize people against Tiberium (and the fact that Nod elite units like the Black Hand, Shadow Teams, and Commandos decline to make use of Tiberium Infusion leads me to suspect that the "upgrade" has some sort of horrific long-term side effects). Bringing data from C&C4, it's noted that even with the terraforming projects related to the Tiberium Control Network, there is still trouble getting clean water to grow crops.
B. Is it remorse that he killed her, or remorse that he got played?
So in other words, it's just another example of Nod's habit of killing civilians and then pinning the blame on GDI. Of course, here, it's Nod's own people that Kane is slaughtering wholesale.