Dropping support for the PS2 is a red herring.

Final Fantasy XI is first and foremost a PS2 game, it was written for that platform first. And when it came to other platforms, the game wasn't rewritten from the ground up, but was instead ported to the PC (and from the PC to the Xbox 360). No matter what you're playing FFXI on, everything under the hood of the game, from mechanics to graphics, is at its core PS2 code. Simply disallowing PS2 hardware will not change the PS2 legacy for PC and 360 players.

So, really, what you're asking for is one of two options:
  1. A kludge fix, on top of a kludge, on top of another kludge, all onto a system of code already being held together by liberal amounts of duck tape and chewing gum. You're talking about a game written for the PlayStation 2 and then ported to Windows 98. At best, solutions won't be as elegant as you would prefer. Realistically, there will be new problems caused in the name of "trade-offs," and the "solution" may be worse than the problem.
  1. A total rewrite of the code base from the ground up, a "Final Fantasy XI All-Stars" or "Final Fantasy XI: The Wiley Wars." It involves almost as much work as making a new game entirely. It involves almost as much money as making a new game entirely. And this for a game that has a declining player base, in spite of a price tag as low as $10 (or $5 digital download)? Even if the publisher in question weren't hemorrhaging cash on Final Fantasy XIV, Adam Smith would have words for you.

Final Fantasy XI is almost a decade old. It's showing its age. Continued support of the PS2 isn't your problem, the passage of nine years is your problem. And unless you have a flux capacitor lying about, there is no fix for that, not even if you scapegoat PS2 players.

"If only id would drop support for DOS, Doom II would look and play like Halo!" It doesn't work that way.