Hi Dude,
First of all I didn't understanding your question completely.
My understanding is like this, Org1 has S4B deployed, People from Org2 need to join a conf hosted on Org1. If any person from Org2 calls the Conf join DID no, same number is showing up as same number since Org2 Telephony is designed like that.
If this is your case, I dont think you can do anything on this. Best workaround would be joining meeting from web app or Lync client where you can provide a guest name.
If the user joins from Org1, he can use his extension and pin to authenticate, so that the conferencing window would show users Display name instead of number.
In WebEx conference I have noticed an option to sync dial in phone call with PC webex client, where you would have a name by dialing few digits displayed on screen. I dont think that feature is available in Lync.
If my understanding is wrong please correct me and lets think about a solution.
MvH