...what harm is caused during this duration of time if the alternator main circuit is still connected to the battery, as my original question asked?[/b]
The "generally accepted" problem is one of damage to the alternator; alternators REALLY WANT to have some kind of accumulator to dampen the positive and negative spikes it produces, and that's the battery's job. You disconnect that battery from the equation and you run the risk of alternator damage or possibly runaway.

"Runaway"? From a safety aspect, theoretically an alternator-equipped car can continue to run with the battery disconnected. The car will run as long as the electrical system has voltage; the alternator will continue to put out voltage as long as the field circuit is "excited"; the field circuit will remain "excited" as long as the alternator is putting out voltage. See the Catch-22 there?

I've never tried shutting of my car with the kill switch without the alternator/ignition properly wired, so I can't say that's what will happen for sure. But I certainly don't want to try it on my car. Maybe this is a good one for Mythbusters?

The goal is to get the car to stop running, with all electrical equipment de-energized. You'll do that either by stopping the alternator from turning (by shutting off the ignition) or getting the alternator to stop putting out electricity by opening the field circuit (thus killing the ignition due to lack of electricity). Either way works.

I can assure you that, upon presenting your car to an SCCA tech inspector for its logbook, one of the very first things the inspector will do is ask you to start the car then he/she will reach over and flip off the master kill switch to see if the car stops. If you're comfortable having someone do this using just the battery circuit, and it works, then you're all set... - GA