The kid had fucked up, so to speak. Even though you could see that Nucky liked him, he knew he needed to kill the kid, because otherwise it might have been regarded as a sign of weakness. He needed to make clear that nobody can steal his booze and get away with it.
I also got the feeling that nucky wanted to in a way prove a point to Owen. Im not saying that swayed his decision but i sensed alot of tension between them two. I think the fact that Nucky has been stabbed in the back so many times before by close people and when he saw mickey ask Owen his opinion just after he gave orders he might have been wanting to show Whos boss still.
'As far back as i can remember, i always wanted to be a gangster'
