There might be a bit of confusion around this whole thing.
Dynamic sites (such as ffxiah.com) are vunerable to
code injection. This is a form of attack in which a dynamic site calls on certain data, but the attacker spoofs that data to inject their own code. In this case, a flash/script to redirect the end-user to a site that could have possible exploits that will automatically download to the end-users computer.
FFXIAH.com probably didn't have any of it's sensitive data stolen or corrupted and the code itself was easy enough to erase. I'm sure Scragg is altering the php right now to prohibit that type of injection again. FFXIAH.com is safe, yes, but the people who were redirected unknowingly to the malicious site might be infected. They might have keyloggers or dataminers.
Alyria, I think there might have been a misunderstanding when the thread started - Although the box is "annoying" to look at, people were by no means upset that they had to look at it. They were upset because it implied that the server had been compromised. If you remember ffxi-somepage, that site hasn't been the same since it's ad attacks.
Suggestion to anyone that visited ffxiah.com and might have been exposed: AV scan your computer a few times. Make sure virus definitions are up to day. Might want to consider not logging into FFXI for a day or two, so that you give the AV companies enough time to identify the virus (if it's new) and create something for it.