It does disable it with low fuel or engine not being up to temp and other factors. I would recommend disabling though because the auto stop start does not actually save on gas and is very hard on engines, especially turbo charged ones. Turbos need a spool down time before they are shut off...
There is a fail safe in it. If you should happen to stall release the clutch all the way and then depress the clutch all the way and it should start back up without having to push start button