git rm --cached submodule_path # delete reference to submodule HEAD (no trailing slash)
git rm .gitmodules             # if you have more than one submodules,
                               # you need to edit this file instead of deleting!
rm -rf submodule_path/.git     # make sure you have backup!!
git add submodule_path         # will add files instead of commit reference
git commit -m "remove submodule"