For long term storage draining the tank & running till all fuel is gone was recommended in the winterising procedure.
There are two ways to stop the O&R engine, one is the brass stop switch on the back of the magneto plate (exhaust side) or a remote stop switch (used on some tools), both of these short-out the primary of the magneto. The second method is to close the choke (as you mentioned). On early engines there was an optional third method, a shorting strip for the top of the spark-plug, shorting the spark-plug can be used if other methods of stopping an engine have failed (usually with a well insulated screwdriver).
Here is a picture of the brass stop switch,
And the (optional) HT shorting strip on an early engine,
David