Yes, the translators do change the underlying metadata structure, but all the metadata elements should still remain. You should be able to just use the "FGDC to ISO 19139" to get to your desired ISO format. As for the Metadata Importer, my tool does use the import metadata tool. This is set automatically for you based on what export format you use. For example if you use the "FGDC to ISO 19139" export, my tool is designed to make the changes then it will import the updated metadata back to the target using the 'FROM_ISO_19139' translation (since it was exported to ISO format, it will be imported FROM_ISO). This is precisely why I have it set up to have a source parameter and a target parameter. You can set these to both the same feature class to update the original, but I set it up so you can create a back up as the target and use the original as the source so you can perform the metadata update and compare the original metadata to the updated metadata to make sure everything is there before changing the original metadata. Below are the dictionaries the code uses that choose the appropriate import based on the export format parameter:
# Set up export and import types, import is derived from export type
export_dict = {'ArcGIS to FGDC' : 'ARCGIS2FGDC.xml',
'ArcGIS to ISO 19139' : 'ARCGIS2ISO19139.xml',
'FGDC to ArcGIS' : 'FGDC2ESRI_ISO.xml',
'FGDC to ISO 19139' : 'FGDC2ISO19139.xml',
'ISO 19139 to ArcGIS' : 'ISO19139_2ESRI_ISO.xml',
'ArcGIS or ESRI-ISO to ISO 19139' : 'ESRI_ISO2ISO19139.xml'}
import_dict = {'ArcGIS to FGDC' : 'FROM_FGDC',
'ArcGIS to ISO 19139' : 'FROM_ISO_19139',
'FGDC to ArcGIS' : 'FROM_ARCGIS',
'FGDC to ISO 19139' : 'FROM_ISO_19139',
'ISO 19139 to ArcGIS' : 'FROM_ESRIISO',
'ArcGIS or ESRI-ISO to ISO 19139' : 'FROM_ISO_19139'}
My tool really only has 3 basic processes:1. exports metadata to desired format as a stand alone xml file2. does the find and replace text operation on the stand alone xml file3. imports the updated xml file back into the feature class