I like that idea. A nuclear wasteland is returning Earth to its natural state.
When you're dealing with geologic timescales, a nuclear winter is just a minor hiccup. You can expect something a meteor impact or a super-volcano eruption every few million years. It's no biggie. The hard part is killing all humans, which I supposed would require channeling the initial deaths to power a genocide spell.
Also, splitting up the cast and pairing Elana with Damon instead of Stephan would be a good excuse to have Elena/Damon pegging scene with MFF.