This whole incident seems all to familiar to what happened to Quake. Before the game was even released, someone had given someone a password to a secured section of their FTP, and they got a hold of the quake source. It was then released between some people (not as many people compared to now since distribution methods and the internet itself weren't as mature) and some linux gurus got a hold of it. They did what they needed to do, and released a version of quake for linux before Id had even released the windows version. This is evidence for anyone that says that this whole thing will kill Valve and Half Life 2. This same thing happened to quake, and look where quake went, and where it still is today.
On another note, I gurantee that this also won't affect the way we play Half Life 2 online, as far as dealing with cheaters and such. Valve was fully aware of this problem, and more than likely assumed this would happen before anyone of us knew about it. Hell, it was stolen on the 19 of September. That was a full 13 days before we even knew about it. They aren't stupid, they will modify the crucial parts of the source so that once the game is released, the old source will be worthless. Oh well, I know that I will go out and buy this game the day its released no matter what happens between now and then. My father once said, (actually always) "Life's a bitch, then you die."