You must have missed the point that flash chips, used in this application, can never be secure. It is precisely due to the use of flash chips that this exploit is even possible; can't overwrite a ROM. At the very least, there needs to be a physical switch that enables writing, and the system should refuse to boot into anything but the firmware update screen if that switch is in the "write" position. Better yet, have the switch only function to set the value of a gate and latch that value so that toggling the switch with the system powered up does nothing. The gate's only input would be the switch and it would only read on power-up. Then, the user doesn't even have the option of accidentally enabling write mode once the system is booted, which would protect against exploits such as this, even in cases where the user flips the switch after booting.
Doesn't protect against someone with physical access, but it does change the game to require the attacker, and not just the attacking device, to have physical access or, at the very least, convince the user that there is a firmware update so they're likely to boot into write mode. Of course, write mode could disable all ports except for one USB port and only support USB disk devices on that port.
That wouldn't be perfectly secure, of course, but it'd sure be more effort than mailing your victim a new ROM chip in official looking packaging with instructions printed on forged letterhead. Yes, that's right, even the physical socketed chip solution isn't secure if you think outside the box.