I remembered this thread where the issue wasn’t really solved. We should have reported this as a bug last summer.
Ton fixed this problem today. He’s asking for testing and input. Now’s a good time to report any other issues.
Revision : 53762
Author : Ton Roosendaal (ton)
Usability:
Using Proxy Armature on groups: an Undo now doesn’t force a complete re-evalution
of this system anymore, so posing works similar as for regular (non linked)
armatures - an undo step goes back to the previous pose.
Before, an undo made the entire armature go to rest pose. Bad bad 
I need animators to carefully check - report back if there’s other issues!
Tested on Gilga character from Tube Open Movie.
@RailroadBill: The protected layers are used to restrict what can be accessed/changed in the linked proxy.
-LP