Top POI's are effectively removed from a player due to the fact that they are targetted by the Fortress and are invariably in the hub ring.
Removing all bonuses from a player after killing a fortress still seems like a punishment. What is to stop an alliance collectively deciding to control the centre, but not kill the fortress, in order to prevent other alliances gaining a badge? They may not get the badge, but they'd still block the centre from other players and the opportunity to kill the fortress from weaker, less efficient alliances.