At the risk of repeating a tired Internet cliche, I think the leak may have helped Half-Life 2.
If the project was already months behind schedule and had a year before a GM build would be ready, having the source code leaked may have given hardcore gamers reassurance that the game was actually coming along and would be finished at some point.
Of course, there's also the newsworthiness and buzz coming from the leak itself.
How does reassuring hardcore gamers that the game is actually being made help Valve? Do you think they would have boycotted the biggest game of the decade simply because it was released late? Seriously... how did this help Valve? I know everything worked out well in the end, but the leak did somewhat spoil the game for a lot of people. I certainly didn't appreciate it at the time.
I suspect Duke is one of the reasons for the complete lack of E3 related announcements so far this year. That and their own Portal 2. They'll not want a "coming next year" annoucement about E3 to be wasted by it being overshadowed by the big things being released in the next few months. Hopefully there will be an announcement later in the year, during one of the release dry spells.
Though you could be right, we've already been waiting for E3 twice as long as E2.
At the risk of repeating a tired Internet cliche, I think the leak may have helped Half-Life 2.
If the project was already months behind schedule and had a year before a GM build would be ready, having the source code leaked may have given hardcore gamers reassurance that the game was actually coming along and would be finished at some point.
Of course, there's also the newsworthiness and buzz coming from the leak itself.