The certs listed in libnss are not maintained by the same people as the
certs in ca-certificates, so making libnss use ca-certificates isn't
really an option.
So...why don't you just remove the CA using the application that uses
nss?
For example, in firefox, Edit/Preferences/Advanced/View Certificates,
and use the "Delete" button.
** Changed in: nss (Ubuntu)
Status: New => Incomplete
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system wide libnssckbi.so does not reflect /etc/ca-certificates
https://bugs.launchpad.net/bugs/593320
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