git filter-branch reports unstaged changes

I can't be sure this is due to git-crypt, but I've never experienced this before.
Steps to replicate:
- add a file to working dir
- add .gitattributes to select file for encryption
- add file to index
- commit
- push
- try to remove file from history (git filter-branch --tree-filter 'rm -rf path/to/file' HEAD

Expected results:
- history rewritten to never mention the said file
- file removed from origin

Actual result:
error message `Cannot rewrite branches: You have unstaged changes.`

`git status` returns

```
On branch master
Your branch is ahead of 'origin/master' by 1 commit.
(use "git push" to publish your local commits)
nothing to commit, working directory clean
```

Anybody else experiencing this issue ?

I reiterate that I might be wrong, and this might not be due to git-crypt, but I can't think of any other cause.