Depois de muita tentativa e erro, a seguinte receita funcionou:
# tag the root-most commit so we can reference it
git tag root 'git rev-list HEAD | tail -1'
# check it out on its own branch
git checkout -b new-root root
# amend the commit
git commit --amend
# now you've changed the commit message, so checkout the original branch again
git checkout @{-1}
# and rebase it onto your new root commit
git rebase --onto new-root root
# then nuke the temporary branch and tag we created
git branch -d new-root
git tag -d root
o crédito verdadeiro deve ir ao #git para esta resposta.