My wife's car has that; I find that if I stop and keep my foot very lightly on the brake, just enough to stop the car rolling, it doesn't shut the engine off. If I step more firmly on the brake while I'm stopped, it shuts the engine off.

Also some of the diagnostic scanners will have a way to disable the auto stop/start, or so I've heard. I have a scanner but haven't tried it on her car.