Yes, you can replace just the synchro(s)...
Yes you can replace just the synchro(s) in the tranny. Do you have a place to pull the tranny yourself? Call around to some indy tranny shops and see if they are familiar with the Getrag manual tranny from your BMW. Tell them what it's doing and get their recommendation. You'll save some money if you can pull the tranny yourself, but if its not worth it to you just let the shop do it. How's your clutch? Good time to replace that too while your at it.
The Bentley manual has a good blowup of the manual tranny if you want to look at it.