Upvote:2
In my research I found this excellent article by Zeev Goldmann who argues that the famed synagogue that was unearthed and the ruins beneath it indicate that the city did in fact repent and turn to Christ:
http://zeevgoldmann.blogspot.com/2008/08/vi-capernaum-synagogue.html
So this is a case similar to that of Jonah, where he predicted the imminent destruction of Ninevah but they were spared when they repented.