I think you need to actually use FieldMappings.replaceFieldMap to get it to persist. Example from help topic Mapping input fields to output fields:
# 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)