Maybe a system like this would make sense if all the towers were active. If there was a mob at a tower I would understand. I know the occasional mob at MoD happens. But as it stands, people are getting punished for playing the game. It is not my fault that, for example, there are only the same five PKers while my guild defends Sards. I am not trying to boost, it just so happens to be that five random people are all I have for variety. Since I have such a limited variety, I get punished. That is not the right way to do it. Whatever this is system trying to prevent, it is not a fair system.
If the goal is to stop mob PKing in towers, disable PKs counting in the specific levels that they are happening in. If the first floor of MoD has a mob happening at the doorway, disable PKs counting on that specific floor. Let the flag room count PKs.
Perhaps someone can clue us in on what this system is trying to prevent? I imagine if we knew what the purpose of this really was, we could put our heads together to come up with a better solution. It would be more beneficial than playing a guessing game.