In fiction we can often assume that bad things, particularly terminally bad, won't happen to good people, but it is compelling when fiction mimcks real life where bad things often do happen to good people.
I wouldn't exactly call Eddie a good person. Apart from the things we learned about his past in this episode, he apparently had no qualms about being part of Nucky's criminal empire.
I'm unclear on what deal was cut in regard's to Eli's son. They arrested Clayton but what will keep him from telling the truth and thereby implying Eli's son in the accidental poisoning of that other kid?
But maybe we'll hear more about that in the upcoming episodes.