I did connect an external WordPress website to wordpress.com by using Jetpack. Later I decided to remove the website, for good. I was not able to delete it from "My Blogs", I created a new post in the forum asking about it. It turned out that a staff member had to do it manually.
A feature letting the user delete a jetpack connected site from "My Blogs" would be handy, it would cause less clutter in the forum, and it would be less work for your staff. It's a win/win feature that should be implemented IMHO!