How to remove an entry with null sha1 in a Git tree

Question

I have inherited of a git repository with a null sha1 for a commit entry in a tree, preventing FishEye to index the repository.

$ git fsck
Checking object directoriies: 100%(256/256), done.
warning in tree db22a67df70dc4ff90ec4cd666da91e9c2cb0d9:
    contains entries pointing to null sha1
Checking objects: 100% (416532/416532), done.
Checking connectivity: 416532, done.

Looking for the given tree give me the following result:

$ git ls-tree db22a6
100644 blob e615f18b55a39f2719112ce209c2505dd92d8e75    .gitignore
100644 blob ac852f06c5a04420356c1d5efca44d9a864e78b0    .project
160000 commit 0000000000000000000000000000000000000000  SomeDirectory
100644 blob 631c17e28026261a2ccf6bc570842cf4af9f181c    GoDeploy.bat
100644 blob 40e992ab5c3868af2910135c3ac4610c3646e7f8    pom.xml

Looking in the history, I've found that SomeDirectory was initially a git submodule and that the commit that seems to cause the issue is the one that removed both the .gitmodules and SomeDirectory. Now, there is a real directory called SomeDirectory at the exact same place where the culprit was.
I though I could still try to fix run a git filter-branch to see what I would end up, but it does not work:

$ git filter-branch --force --index-filter \
$ 'git rm --cached --ignore-unmatch SomeDirectory' \
$ --prune-empty --tag-name-filter cat -- --all
[... striped out for clarity]
Rewrite c571a3ec94e9f84471577bac41ac7375c729ef08 (76/18522)error:
    cache enttry has null sha1: SomeDirectory
fatal: unable to write new index file
Could not initialize the index
[... striped out for clarity]

What am I supposed to try next, knowing that there is no backup that I'm aware of prior to the commit that causes the issue.