Well :-)
Plugging cables in the sound output plugs when the amiga is on SHOULD NOT be a problem as the Amiga sound circuitery and cinchs are made for.
You should investigate around the modified plug to eliminate possibles shorts, I suggest you mount some Amiga style plugs back instead of the jack the other used.
Making a small adaptator cable or soldering two male cinch connectors to the speakers cable would not be too hard to do :-)
if you find no shorts, it's possible that the sound mixer ic (near the output) or the audio capacitors might be blown :-(
A more horrible thing to might have happened would be the death of paula too :-(
You should pray for the shorts on the plug...