I did some further testing and the trick for me was simply to delete everything within each of the individual ROM folders for each system (SNES, N64, etc.). I elected to leave the readme.txt file for future reference.
On my next boot, I only saw the games for which I had ROMs store on the Pi.
I'm not sure why you were getting an error message about read-only access though - I would start by troubleshooting that because I had no issues deleting files/folders.
Hope that helps!