Is that what you really want to do?

What's to keep an OS upgrade from restoring the certificate?

A system or user-maintained blacklist seems like a more tenable solution. You don't want to delete the cert, you want to hang a scarlet letter on it. Oh, and not trust it for anything (or better, use it to blacklist any site that attempts to use it).

At least for me there's no such choice as delete in the System Roots keychain. The only thing I can do is to set it to "never trust" and still Chrome/Safari show it as trusted: http://imgur.com/NcUYf

Did you try that and it really removed the CA?

Or is it supposed to remove the trust only but keep the entry?

It removed the entry completely from the Keychain, I am on Lion for reference.

Sanity testing by loading the homepage over HTTPS results in a certificate warning on all browsers (Firefox redirected to HTTP).

Right-click delete is not an option on Snow Leopard, for some reason.

Firefox uses its own CA store, so you need to remove it there too (or wait for the 6.0.1 update).