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since the blowing up issue was because 12V came into the 5V pin on the Gotek power connector, for a very simple protection, you could add some kind of voltage regulator to the 5V input. Cut the trace leading to the electronics and between the power input connector and main voltage trace add in maybe something like a LM7805? There may be more elegant ways, perhaps some kind of current limiter or voltage limiter IC that's in a small transistor type package?
The other thing you could do is simply remove the cheap crappy old motherboard floppy power connector pins and fit in a new proper type connector with the tab to stop it being plugged in backwards. They are available on ebay pretty cheap. I have changed that connector on all my Rev 5 motherboards to avoid that exact problem ;-)
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