I previously opened this as a bug and discovered that this was an intended feature:
Did a test with my guildy after exiting the guild. He let me know that his King production was ready. I won the battle but the King could not be plundered, only the non motivated buildings could.
I have a problem with this feature and I think most of the top players will. Let me elaborate:
Since most of the InA towns held by top players need around 50 motivations per day, this feature makes plundering impossible. These towns get all their buidlings motivateded long before productions are ready.
Guild Wars without plundering will get old pretty soon.
The game will be only about who has the time to do more battles against weaker opponents and who can farm more supplies.
Inno should seriously change this if they want to make the game interesting for top players.