I'm not sure if replication is your end of the day question - or if it is that someone doesn't want people on Server A to be able to send email to Server B (for example).
If it's the second problem, the work around I can think of would be to create a dist. list (DL) called "Server A" (or something) and put in it all the people/mailboxes on Server A. Then on the DL's on Server B - on the "Delivery Restrictions" tab, you can reject messages to this DL from anyone in "Server A" group(DL).
This wouldn't keep it from being replicated or visible, but it would keep use of these groups limited.
Good luck -
aliciaJ