I looked at the '88 diagram on the Tom Collins site, and there is a resistance wire to the alternator. You understand this is different from the resistance wire to the ignition coil? The resistance wire to the coil takes the place of the ceramic block ballast resistor used in earlier years. The ballast resistor is meant to limit the current to the coil and has no effect on back-feeding.
The MSD module uses a separate power feed to the module. The coil wire is only used to turn the module on and off. The heavy wire to the MSD is hot all the time (going directly to the battery), and the module on-off depends on the coil wire. I don't know how your Holley ignition is wired up, but if it's like the MSD, there's no path to back-feed.
A relay is usually used to handle the heavier current load you might need for the new module. A relay could stop the back-feeding problem if the circuit is backfeeding through the main power feed, but I suspect that's not the problem. The existing Duraspark module power wire should be sufficient. The Holley tech likely does not understand that you are using the power wire from the Duraspark module to run the Holley module. This should be sufficient to power your Holley ignition. Again, if it turns on and off by the ignition switch, it's not controlling the ignition power, but being controlled by it.
You can test whether the relay would make a difference by purchasing a relay and connecting its coil (not the contacts) to the ignition.
https://www.parts-express.com/12-vdc-wa ... t--330-079 Ignition on, relay closes (test with your multimeter). If the relay then opens when you turn off the ignition and the engine keeps running, it likely will help with the run-on. If not, it's going to do nothing.
Another easy test would be to disconnect the alternator and start the car from the battery. You'll need to pull the plug out of the back of the alternator, and remove the big red wire. Careful with those wires - they are connected to the battery, so tape them off and put them out of the way. If the Jeep shuts off with the alternator disconnected, you've found your problem.
To pick a diode, just make sure the voltage and the current rating are more than what you need. For example, this diode
https://www.allelectronics.com/item/d61 ... ode/1.html would be fine for anything under 6 amps like the alternator connection.