CommandConfig is not what you want. "Springie rights set to 0" is a punishment that is supposed to change rights level for a
single user, changing CommandConfig would change the
required level for
all users.
There isn't a separate user rights file, that info is in the db as
Account.SpringieLevel. There's
GetEffectiveSpringieLevel() that takes punishments into account.
Springie uses User.SpringieLevel at
https://github.com/ZeroK-RTS/Zero-K-Infrastructure/blob/master/Springie/Springie/autohost/AutoHost.cs#L228. That's set in zk lobby server at
https://github.com/ZeroK-RTS/Zero-K-Infrastructure/blob/master/ZkLobbyServer/LoginChecker.cs#L241 and you can see it uses plain SpringieLevel instead of GetEffectiveSpringieLevel(). If you already have the testing environment up you should check if that fixes it, if not you should work on getting it up first.
One problem remains: the user will need to relogin for the punishment to take effect. That's already true for mute, so this doesn't change much, but for bonus points zkls should watch for punishment changes and update mute, springie level and kick banned users accordingly.