If you are sending the exact same message out thru the send port then you may be able to use a flat file assembler in the send pipeline. Do not specify the schema on the Flat File assembler and it will check the BTS.MessageType in the message context and use that schema to convert to a flat file. Even though you have declared the message as type XmlDocument in you orchestration it will still have the message context properties created in the receive pipeline.
If you copy the message in the orchestration you will lose the context properties, so you will also need to explicitly copy these as well
e.g.
outputMessage = inputMessage
outputMessage(*) = inputMessage(*)