We already have a start there. Make all NON-EV certs free.
Also on Chrome at least certificate pinning should prevent that particular scenario.
As to the whois thing, what is stopping me from hijacking a domain, changing the whois and then generating keys? The webadmin might never even know. You don't even need access to their email.
Or to put it more realistically: What is stopping the NSA from pressuring a domain registrar into altering the whois for a brief period in order to generate MITM keys?