Well, that can't really be the problem. Ryan Gordon mentioned that whatever the problem is held up the retail Linux dedicated server package and was removed. The same functionality was not removed from the demo dedicated server package. GameSpy makes up the core multiplayer backbone for the game, they can't just remove it.
I just can't understand this with any software being written in modular form. Whatever was holding up the port just couldn't have influenced the game itself, unless it has something to do with networking. It's probably a legal hurdle.