Is this enough to block this attack? That is, is a "cleaned" system vulnerable to a USB device?
of course it is, because the USB DCI attack is one level below the Intel ME. Even if it is deactivated via HAP, which basically simply puts the ME code into an infinite loop or a CPU halt state - both can be reversed by JTAG.
If they have full debugger access to what's running in Intel ME then removing the code from the firmware probably doesn't make a difference (assuming they can run un-trusted code in that context). If they cannot write their own code and so an attack requires ROP gadgets then removing the code might make it harder (or impossible) to do, but I doubt it.
[1]: http://www2.lauterbach.com/pdf/directory.pdf#M8.newlink.DIR6...