In my opinion losing the PP is very annoying but not so crucial like losing one of the other building. So when i played the last time on Walls and our team was able to blow up the enemy PP, i got an idea for a different penalty when a team lost its PP.
In the orginal C&C Games your base buildings are taking damge when you have a power outage.
I think this function would also fit to Ren-X: When a PP got destroyed, the buildings of its team are getting every Minute 1% damge until the health of the buildings are down to 1%. To clarify, I am talking about the health of the buildings, not its armor. Thats means the buildings are constantly bleeding down under their armor.