There's unfortunately nothing (strongly secure) that we can do about this. This isn't supposed to be a cop out answer, there's really no way to accomplish this on current hardware. We talk to the keyboard through the host OS, so if the host OS is compromised and running a keyboard logger, it will see the keystrokes. We could try to combat this by interfacing with the keyboard device at a lower level, but so could the keyboard logger.

This is one of the problems that the various future secure hardware proposals (like NGSCB) try to solve, by giving you a cryptographically secure channel to input/output devices. On current hardware, anything privileged in the system can see everything going on in the system.