Officially, there's no way to change a MapService without going through the usual publishing routes. Unofficially, if you can get your script to access your ArcGIS Server's directory folder, you can navigate through the "arcgissystem\arcgisinput" tree to find the definition for your service. Buried somewhere in each service folder is the mapx and/or msd files used to render each service, as well as the service-level metadata files. If you edit every relevant files' minScale and maxScale properties then you should be good! Or you'll corrupt the service. Oh, don't forget mapx and msd files have no public interface so nothing's stopping your process from breaking after an errant update.
