My engine has an idle switch in the butterfly valve assembly that the ECU uses to know when it needs to do its idle stabilizing thing. You could tap into that wire.
My alternator (Valeo, 90 A) unfortunately only has 1 skinny wire going out of it: the blue one for the battery warning light. Are you guys sure that disconnecting this will turn off the alternator? May it will just disable the self-excitation circuit.
Alternators 101:
http://www.autoshop101.com/trainmodu...or/alt102.html
More alternator circuits:
http://www.alternatorparts.com/under...lternators.htm
There should probably be a short delay between reaching idle and switching the alternator back on to prevent a short voltage blip every time you change gears.