Unfortunately without going back to Windows 95-esk "please restart to install this keyboard" world, I cannot see how you fix this. Even blackholing some input from the HID is only at best a temp' solution (as they'd just add longer and longer sleeps before fake HID input was generated).
I guess you could redirect all HID input to a certain context (like a Virtual Desktop e.g. UAC prompt) until the user accepts it. However realistically most users would ignore this warning and just click "install" without reading it or understanding the implications.