remove file from all git history
I think what happened is that you forgot to tell other users of this repo not to merge their changes to the new history, but rather to rebase.From the document you quoted:
Tell your collaborators to rebase, not merge, any branches they created off of your old (tainted) repository history. One merge commit could reintroduce some or all of the tainted history that you just went to the trouble of purging.
Try running the same script again, and see that no one re-introduces the old history by means of merging his/her local changes to the new head.