For posterity, note that this will fail if your home directory isn't empty. To get around that, clone the repo's working directory into a temporary directory first and then delete that directory,
git clone --separate-git-dir=$HOME/.myconf /path/to/repo $HOME/myconf-tmp
cp ~/myconf-tmp/.gitmodules ~ # If you use Git submodules
rm -r ~/myconf-tmp/
alias config='/usr/bin/git --git-dir=$HOME/.myconf/ --work-tree=$HOME'