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I'm pretty sure a diode on the output wire would solve the problem the discharge problem. However:
If you do this it probably messes with the voltage regulator. This is a modern alternator and it contains the regulator too or do you have a separate unit for that?
The diodes in the alternator should be designed to handle the voltage spikes. This is a really important, crucial job. If there are problems in your wiring you can have an "alternator load dump". That means it's charging and loses it's connection and will make a huge power spike. I think the spec for this is hundreds of amps and also hundreds of volts. It will act like an ignition coil. So voltage spikes should not be an issue...
The alternator warning bulb is part of the regulator circuit sometimes I think, it's involved somehow. Maybe somehow you are getting mixed parts? Diode packs for older alternators or something? This stuff has been pretty standard for a long time now, I think.
Sorry no real help here....