We were an exception to the rule - my wife moved around a lot and bounced between parents and grand-parents (none of whom lived in one place very long), so we had it in my hometown instead. The church was available, the reception was in my parents' back yard (we had a big event tent set up in the side yard, just in case, but it wasn't needed that day.)
If her family had been a bit more stable, we would definitely have followed the rule of thumb, and we really didn't go to plan B until we discussed it with them first and realized plan A wasn't going to be viable.
There are always exceptions.. and yours is a perfect example. I went to a wedding where the bride had it in her “new” hometown. Since she lived there 10 years after college, she was very happy in that church and area. Her family didn’t mind whatsoever. :)