Unpublishing does seem to lower the chances for a zombie but it still happens.
Over the beginning months of being an admin I tried to permakill all the deleted stories I could and I still had like 40 zombies or so after it was done.
Of course that was like back in 2016 when I cleaned all those up, I’m sure the deleted story horde has only grown again and also mixed with the indestructible zombie stories.
Until the 500 Internal Server Error is fixed, the best you can do is edit the front page of a zombie story and change the title and description. The story itself is still gone anyway, only the front page hides its true empty shell.