While it may seem head-scratching that a company can sell out of a digital product, ArenaNet says that this was done to ensure enough server capacity for the event. The good news is that GameStop and Best Buy are still accepting prepurchase orders, and it looks as though ArenaNet will resume taking orders through the website once the beta weekend is underway:
We limit sales to ensure we have enough capacity for our customers. We're likely to have capacity available after the initial crunch at the start of the weekend. Players who purchase when we're able to resume digital sales at buy.guildwars2.com will still be able to play for the remainder of the weekend.The team has also announced that world transfers will be free and unrestricted during this beta event.
[Thanks to FlyinBuddha for the tip!]