Because the most popular browsers (at least Chrome and Safari) generally require CT logged certificates, if you want to successfully perform a MitM attack against any user, even just some individual user, even controlling a CA, you still can't do so without publishing your fraudulent certificate to a CT log.
This is the important function of the CT log. It is an effective balance against compromised CAs and governments that might abuse CAs, because it causes such attacks to become quickly tamper-evident.
I don't think it would be possible for a system like this to be effective without publishing the actual certificate to the log.