Do you have a new alternator? Perhaps a 1-wire alternator? When I installed my new 1-wire alternator (which incidentally has MORE than 1 wire!?), my engine would run-on when I turned off the car, and I also had to stall it with the clutch.
The solution:
I installed a diode (Radio Shack P/N 276-1143) in SERIES with the wire for the warning light (alternator's #1 terminal), with the diode's "band" toward the alternator (i.e. the wire that you attach to the banded end of the diode to goes to the alternator, and the non-banded end goes to the warning light).
As an FYI, when selecting a diode, you want the voltage to be at least 3x the operating voltage of the system, and the current rating (amps) of the diode should be at least 1.5x the current that the diode will normally see when installed.