I used to play on a Mac, and used something like this to get WoW to run fullscreen on a display other than the primary display (which the game just wouldn't do otherwise). Should work to run WoW on the one half of the monitor too.
[s]If your custom w/h changes the aspect ratio, you need to manually set the gxResolution in WTF/Config.wtf to match or the game will look squished.[/s] Edit: I'm vaguely remembering now that WoW was stubborn about changing it's aspect ratio (and instead would honor only the width in this script, and set it's own height). Sorry I'm not in front of the Mac right now, but I'll try to dig up the solution I eventually found this evening.

Code:
tell application “World of Warcraft”
activate
  set the bounds of the first window to {x, y, w, h}
end tell
I'm not sure how in applescript to specify which World of Warcraft since you'll obviously have two instances of it running. I know you can rename "World of Warcraft.app" though and the game still runs just fine. But I'm not sure if changing it's name causes problems come patch time or anything, since I only tried it a few times to see how effectively my old Mac could run two WoW instances (verdict: very slowly).