True, the computer/USB source and the controller board must share a common ground through the USB cable and connectors to be able to communicate.
But there seems to be some non-trivial common mode voltage difference between the two devices here to cause that much damage.
The problem could be that there is some issue with the way the board is connected to ground (not neutral I hope...!) through the printer's internal wiring and mains power cable connector.
Or perhaps the printer's power input connector is not properly wired.
Or perhaps the computer that hosts the USB source is itself mis-grounded.
An idea to check-
Connect the computer and printer (power switch off) to the mains sources but do NOT connect a USB cable between them.
Using a voltmeter (preferably a DVM), check between some grounded spot on the printer board and the chassis of the computer.
If there is anything more than a few volts present, there may be a problem as described above.
If it is more or less the mains voltage (not sure where the OP is located), then that is most definitely the issue.
But even if there is a small voltage, it still could be enough to burn things out, or it could just be noise pickup.
To check for that, connect something around a 1k ohm resistor between the computer chassis and the printer board's ground then re-check the voltage between them.
If the voltage is still there and is more than half a volt or so, a grounding problem exists.
Use caution when doing this of course just in case there is a serious grounding problem that could create an electrocution hazard.
There is clearly a lot of energy coming from somewhere.
If all of that checks out OK, turn the printer's power switch on and carefully check again.
As far as leaving the 12 volt end of the PSU isolated from the mains ground and neutral, yes that is one way to help reduce risk in this situation.
However the root cause should still be located and corrected.
For checking the old stepper sticks, do all of the above and fix the main issue first with none of them plugged in.
Then with the motors disconnected try plugging them in one at a time to see what happens (PSU power off when plugging them in of course).
If all of them seem to survive, set their currents per Dustin's video and only then connect the motors.