Each time an ArcGIS application closes, it saves a model with all the processes that were run during that session. This model is stored in a toolbox named 'History' in the 'My Toolboxes' directory. For more details see ArcGIS Desktop help.
This logging functionality can be disabled for ArcMap, ArcCatalog and ArcScene, but it is not possible to disable it for Scripting. Therefore, all geoprocessing operations occuring in scripts are always logged in the history toolbox.
There is no method or property on the Geoprocessor to disable this.