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It's not bypassing the speaker, it's using IT's output as the input to a line in jack, if you keep the volume low it's fine, if you set the volume too high it depends on the protection circuits that are on that line-in jack.
Connect your guitar amplifier AUX input to the non-wiper terminals of the volume control in your organ.
Run a piece of shielded cable from the organ volume control to a quarter inch jack installed at the back of the organ and you will be able to use standard terminated cables.