It's a pretty complex change. You would need to write an app that would intercept the system calls to flash the LEDs and replace those calls with its own. There have been many attempts to do this on HTC devices with little success.
There is an app called HERMLED that you can play around with which can access both LEDs on the Mogul, but it has its own issues. My app, LED Killer, only suppresses the flashing service LED.
There is a registry hack out there that suppresses the flashing service LED, but it also kills the vibrate function as they are intertwined.
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