It might be a presumptuous for me to guess, but it likely has to to do with server architecture rather than malice towards the Aether server cluster users. The housing servers that people are afk crafting in are likely shared between the servers on the cluster, the same goes for the lobby and instance servers too. To properly force afkers in Balmung to log off, they have to take down these servers for everyone rather than trying to target the Balmungers in them which is not only more time consuming and inefficient but also far more error proned. At that point you may as well just have an entire server cluster purge rather than just the shared ones, since the server architecture probably isn't meant to deal with the complete absence of the shared servers.

Don't grab your torches and pitchforks yet, these actions are perfectly reasonable when viewed not as an act of malice or malevolence but instead as basic protocols that they perform all the time for forcing people off for maintenance periods.