I think you need to actually use [`FieldMappings.replaceFieldMap`][1] to get it to persist. Example from help topic [Mapping input fields to output fields][2]:

    # First get the TRACT2000 fieldmap. Then add the TRACTCODE field
    #   from Blocks2 as an input field. Then replace the fieldmap within
    #   the fieldmappings object.
    #
    fieldmap = fieldmappings.getFieldMap(fieldmappings.findFieldMapIndex("TRACT2000"))
    fieldmap.addInputField(fc2, "TRACTCODE")
    fieldmappings.replaceFieldMap(fieldmappings.findFieldMapIndex("TRACT2000"), fieldmap)


  [1]: http://help.arcgis.com/en/arcgisdesktop/10.0/help/index.html#//000v0000008q000000
  [2]: http://help.arcgis.com/en/arcgisdesktop/10.0/help/index.html#//002z00000014000000