Actually, the most likely reason is that the game just didn't sell well enough on PS2, and it had such a high budget to begin with, the financially weak Midway didn't want to take the risk of what would end up being expensive ports to GC and Xbox.
And don't assume that games with poor sales were just bad games. That's not necessarily true on any system, even the PS2. Haven was released right in the middle of the holiday rush with relatively little marketing. It's also a kind of multi-genre game whose gameplay is difficult to encapsulate to casual gamers. The lesson to be learned here is that publishers should release games throughout the year, not just at the holidays. Hopefully Zelda will sell extremely well in March and begin to lend legitimacy to this tactic.