I went back and re-watched the scene, Hershal had his gun on him too, I don't think that kid was going to take down two people with their guns aimed at him, his rifle was in one hand not even in a position too shoot. I have to say after carefully re-watching the scene, Carl "jumped the gun" on this one. Perhaps he has seen too many people given a chance, quickly turn to foe's. He has become jaded, even his reaction to the refugee's, his empathy levels are the lowest of the group now. He is just a kid, but has become a product of his environment, and it's a nasty one.
One thing this season has shown it is pure survival mode now, against both walkers and humans, especially those you don't know, and life morality has fallen fast.