Well it wasn't solely Eli that got Jimmy killed. Jimmy contributed a big part in getting himself killed. I just don't get why Nucky just lets so many people slide, like Mickey and Eli, when he just had to kill Jimmy. Jimmy was genuinely remorseful over what happened and wanted to make right on what he did wrong. Nucky could have gave him another chance.
Eli is coming around though, I just don't think his loyalties are with Nucky as his brother, I think its because his plans with Jimmy went south. If push came to shove, I bet he would be tempted to move against Nucky again.