If I understood the original question correctly, I believe that the problem was that the directory contained a mix of repo files and unrelated files that are important.
So in that case, rm -rf on the whole folder could delete the important files also.
Until repo has an uninit/destroy command, here is a workaround:
cd directory
ls -alt directory
The repo synced files should mostly be near the top, so you can just rm -rf on those directories.
The -t option sorts by time, and -a allows you to the see the . files such as .repo/