I'm not quite sure why Firefox won't display the CA certificate in the GUI, but you can manually remove it from the file
cert9.db in your Firefox profile.
sqlite3 cert9.db "DELETE FROM nssPublic WHERE printf('%s',a3)=='LABEL'"
Replace LABEL with the correct value for the certificate you want to remove (usually the subject of the certificate).
printf() function is needed because the data is stored as BLOBs and must be converted to a string before it can be compared to the reference string.
If you're uncertain about what label to specify you can list all labels like this:
sqlite3 cert9.db "SELECT a3 FROM nssPublic"