I have put further work on a back burner for the time being, however I would very much like to spend some more time.
The more I think about it, the more I like the idea of modifying DosBox to output the programmer "commands" to a serial port (USB RS232) as long as I can figure out how to do this inside DosBox. The serial output would connect to the Arduino Mega, which would be able to parse the data stream in order to set the pins and power supplies as just like the programmer would. The timings wouldn't be perfectly accurate, but hopefully would be good enough to get a response from the device.
I will look into "erase" as this appears to be the action people need/want. I did buy 10 EPM7032 devices, so I can sacrifice one and program the lock bit. These particular devices are the later JTAG ones, and I have confirmed that I am able to program them using the cheap Chinese Altera USB Blaster clone.