Maybe not, though I'm not sure.
I recall when Trot Nixon threw the 2nd out ball into the stands on May 17, 2003. I don't recall if it was thrown back or not, which is key in your scenario, but I think the kid did not throw it back. Trot looked over at the ump when he realized his mistake and the ump called time, which, I guess, made the play dead. They may have just issued a ground rule double kind of deal on that play.
This is what happened, though.
1st out.
Molina singled to center.
Davanon singled to left, B Molina to second.
Eckstein flied out to right for 2nd out, and Trot Nixon tosses the ball.
Molina and Davanon take two bases, scoring Molina.
Eventually, after scoring more runs in a traditional fashion, Glaus strikes out for the 3rd out.
I haven't researched the rules yet, but I concur with you. I used to ump some and without getting out the 'Book', I would probably rule a dead ball and award a base to all runners. Whether the ball is thrown into the stands accidentially or on purpose (but mistakenly) shouldn't matter. A wild throw to first that ends up in the stands is ruled a dead ball and the runners advance. On the other hand the Umps have to have some judgement, and must assign intent on the part of the player. I could see an instance where a player intentionally throws a ball into the stands to create a dead ball because he has no hope of getting a runner(s) out.