If you're going to assume they have stealth, then they get the +1d6 to all three attacks. Stealth lasts until you finish resolving the action that breaks it. PHB2 pg 222.
The Halfling Slingers have a specific ability that allows them to attack from hiding without breaking stealth if they miss. Plus stealth is easy to get back if they have cover.
I think this is a good idea. To me stone rain is only scary dangerous when you focus fire. If you have to spread around the damage, its then solid but not outrageous damage.
And therein lies my dilemma. I prefer to play enemies as strategically as I think the opponent would be. I look at the halfling slinger and I think, "Now here is a cunning opponent who will use whatever advantage they can and strike with good tactics in mind."
That means having both halfling slingers in the encounter focus-firing, and communicating and using cover to hide and get combat advantage against the best targets.
This would be much alleviated if the power simply stated that all three attacks must be against separate targets.