Keep lord being under attack should also disable the waypoint. And keep lord being dead should keep it disabled also.
This can only be a good change. As it is, you only promote griefing in WvW by allowing otherwise. As Arenanet doesn't play WvW often enough, they have probably not had to experience the griefing of someone contesting the waypoint on a keep all day. That isn't fun for anyone but the griefer. Little things like this don't help the game mode - there are enough frustrations as it is. And no one enjoys this: "Keep????" "Just someone tagging keep and running by" or "Keep????" then having to spend 5 minutes exploring all of the attack points only to find out no one is there.
This way, an individual player cannot grief and annoy an entire server of players. You wouldn't see any other game allowing this type of behavior when it's so easy to fix. It is not beneficial to the game mode to keep it as is.
Really, just make the change.