One of these days the boys will have to learn their lesson, I love that they save people that they put that first, but if they've learned nothing in the past couple years is that sometimes you have to strike first, and while it's unfortunate this is just a little kid, he could become something much more dangerous. Lilith was in a childs form, and if they could have killed her then before she became a seal, everything would be a lot different. Granted Dean might still be in hell.
but still I doubt the world will be ending. (and no this isn't a lead to should Sam have been taken out ages ago or not, because Sam is different, this kid might not be)