Knowing origin by the ID info isnt metagaming. ID reading can be explained by many ways.
Maybe a not so well chosen example of me. Sure the ID reading can be explained, but there are certain IDs where it is not this easy.
Scan the MND guy and you see an Eagle using civinial guns with an MND ID.
In RP you ask him for his papers and you get, surprise, either Civilian or Corporation/freelancer papers of the are he is operating in.
As long as his cover is not blown due to previous actions, the MND ID is not telling anybody that he is with the MND if it comes down to the RP.
But thats another topic.
My only concern is that those people from the faction will be recognized as such.
Making your shiny new faction popular and known opens up some locked gates to the official way of life.