O-sensie really said that "clean kill" stuff? I would doubt it.
Anyway, my two cents, (which summarizes much of the above) is this:
Aikido is not non-violent, as much as it non-agressive.
Aikido is separated from many martial arts because it (ethically and practically) allows for a proportionate response, that is one in direct proportion to the intensity of the attack.
I think that using chokes (carefully) in practice has two values: 1) you need to experience it before it actually happens so you can know the feeling you'll have while using aikido to get out of it, and 2) knowing how to do a choke may be the ethically kindest thing, particularly if multiple attackers are present, and a quick, non-lethal response is called for.