Sorry -- this make me nervous. Aren't we potentially changing the underlying security process here?
Nope, the login process still goes through Joomla API followed by our API. It's an extension onto Joomlas.
The first thing that I did when setting up me test-bed site was to enable 2FA via the Yubikey -- and I can't see how the CD login willow all me to log in with my current setup.
CB supports 2FA authentication plugins. When "Two Factor Authentication - YubiKey" is published in Extensions > Plugins you should see the Secret Key parameter in your CB Login Module. The parameters for the user to configure 2FA are in their profile edit as part of the "params" field output.
So, not knowing anything at all about extensions, modules, plugins, etc., how easy is it going to be to disable (or even remove) the CB login code?
There's no reason not to use it. It works fine with Joomla authentication plugins as is. There is no official support for disabling it. CBs login process handles email confirmation validation, user approval validation, and anything that acts on CBs login triggers.