Homebrew installation failed on OS X El Capitan. Uninstall won't work. How do I start over and reinstall?
Late answer, but I just ran into this issue myself. 

This Github issue suggests the solution is to run rm -rf /usr/local/.git. I did that, but the issue persisted. I then deleted the /usr/local/Homebrew directory. That seemed to resolve things for me, and I could then re-run the install command OK.