Like the many commenting in #46, I too find it frustrating and a bit patronizing that this tool removes my remotes. I want to point out that there are usages of filter-repo that don't rewrite history. Most commonly, I create a new branch from some feature branch, modify its commits, and then push it as a v2 version which gets merged instead of the original. History is kept intact.
Of course, I still have trouble seeing the value of this protection since Git already protects you from rewriting history (unless you force-push). Perhaps if it would be a compromise to only apply this protection if your branch is tracking a remote?