Wow, it was I who made the Fighter, and I've downed hundreds of them, but never had this total wipeout.
As for the original game, this wouldn't happen because the aliens can only die because of the UFO Power source explosion, and all UFOs are set to have some of its crew be spawned outside. The Fighter is specifically designed to not be like this (because it's a small craft designed for defence, and certainly not for ground missions).
But I wonder what would happen in the original game if it had such a UFO and everyone died inside. Would the game just crash?