The developer is in the midst of testing a fix, including the possibility of restoring any missing goodies. It promised more updates on the situation. The company is keeping the game offline until there's a solution, though, which could leave players waiting a long time -- and it's not certain that everything they earned will be waiting for them when they return.
Update 5:15PM ET: Bungie said it had "validated a fix" for the problem and would roll back accounts to the way they were before the update went live. The game will be out of commission for "several more hours" to implement the fix, the studio said. This is unfortunate if you poured a significant amount of effort into the game after the update arrived, but it beats losing much more progress.
Update (9:31 PM ET): Bungie has completed a "rollback" of player data, and says that the game will be online again round 10 PM ET. That you'll be able to play again is the good news, however any progress accumulated since 11:30 AM ET this morning will be lost, purchases made during that time will need to be redone and Bungie said it will restore any player silver spent between 11:30 AM and 1 PM ET today.