Who said anything about brotherly love superceding all. Loyalty is the stock Nucky trades in on 'Boardwalk Empire' (Sun., 9PM ET on HBO), and once you prove you're all out of it, he's got no further use for you. Even if you're a blood relative.
When Eli came to his brother, sobbing and apologizing and trying to make things right, Nucky told him in no uncertain terms where he stands now. He then proceeded to prove that even though he usually has other people get their hands dirty on his behalf, he's not above getting into the fray.