To disable the driver, you would go under device manager in your control panel, find the device and right click "disable" or "uninstall". If you uninstall, you can click "scan for new hardware" and windows will locate the device and install a driver for it, or you could look it up on Google and do a manual installation.
A trojan could sneak onto an external drive, it's a tricky thing to know without knowing what exactly the behavior of the virus is... The easiest way to do it would be to copy files that you know are not infected from safe mode, and hope that it doesn't transfer.