When I first purchased my Ram I was skeptical of the auto stop/start system because other vehicles I had driven with it seemed like I was driving a golf cart. There was just a little too much delay between when I wanted to go and when the vehicle fully started and moved.
However, with the eTorque, I don't even notice it starting and stopping unless I happen to see the light on the cluster or have the radio low enough I can hear the engine stop running. It's rare that I have my radio that low.
I guess I can't think of a valid reason to disable it.