I just pushed some more debug code, please snag a build...
No sorry, same thing. The next two tries, I reproduced it twice.
Then I went to windowed mode, and couldn't reproduce it after two tries.
I noticed that the crash isn't happening as the game is won or lost. When I played in windowed mode, instead of when it usually crashed, the enemy kept going after my cows, and workers, before the window finally came up "You lose!"
Therefore my inexperienced guess would have to be it has something to do with the destruction of the last structure.