In macOS X Sierra after coming across https://discussions.apple.com/thread/3828655?tstart=0 I was able to delete a VPN item that had a greyed out "-" button, even thought I had deleted the "Profile" it was associated with. I did so by the following commands:
1: In terminal, networksetup -listallnetworkservices
gives a list of the names of the services.
2: In terminal, networksetup -removenetworkservice "name of service in quotes"
will remove the desired service - the quotes are needed to take care of spaces and other fancy characters - they could be escaped with backslashes (\) instead. This might be the bit that messed up the original author.
3: In terminal networksetup -listallnetworkservices
gives a list of the names of the services, hopefully showing that the undesired one is now gone.