If an enemy army has no place to retreat to ( faction/allied territory ), the game might CTD. It mostly occures while manually fighting a battle, but this might happen during the autoresolve too, i guess.
As you have noticed yourself, it´s the most save way to annihilate the enemy completly to avoid crashes. To be honest, i don´t remember how vanilla used to work - it´s too long i´ve played it.

Btw: I´ve got no link at hand, but i remember that i recently was browsing twc forums, and have seen a "warning" concerning the quotes, which seemed to cause frequent CTDs - i wonder if one could get rid of those, even at a price of loosing the citations, and those cool images in the background from EB?