I am used to Mercurial mq extension to maintain a set of custom patches over the upstream. They can be published as a separate repository aside from the upstream. Now in git
AFAICT from the provided link about Mq, it has about the same publish problems as git rebase?
All-in-all I think publishing your branch, with the warning that it is a rebasing branch is your best option. For example, that is how the linux-next branch is maintained.