How would Sapling avoid this? As I understand it it uses the same data model as Mercurial which is really the same as Git's. I think you would need something like Pijul to solve it nicely. At least as far as I can tell.

I might actually try this in Pijul because I too encounter this semi-regularly (it's not a freak occurrence at all) and my solution is basically to give up and squash my branch before rebasing.