I read the book Wiseguys when I was a kid. A few years later I saw Goodfellas, and go, "holy crap that's the book I read." I think Scorecese followed the book pretty fairly, but maybe there was some license.
I read some of the comments, but I think you might be overthinking it. The guy saw something he shouldn't have. The mobster has to kill him. Loose ends are bad. The only thing you need to make the mobster easy to relate to is for his reasons for killing the guy to be equal to or stronger than the guy he's killing's reasons he doesn't deserve to die. The guy he's killing did nothing but see something he shouldn't have. He saw something. He didn't even mean to. He wishes he could forget it. He promises he'll never say a word. Mobster knows that people lie. They get drunk and their lips loosen. Someone leans on them hard and they'll tell them everything they want to know. You can't leave loose ends. He feels bad about it, show it in the way he relates himself to the guy. "He could've been me. 10 years ago, 12, it could have been me staring down the barrel." Let him reflect on what happens if the loose end doesn't get tied. Who gets hurt? Is it just him? Is it his whole family? Is it his mother, wife, child? It's easy to make it look like the mobsters hands are just as tied as the guy's he's killing. That's all you need to do.
Thinking about it most of Lorenzo Carcatera's work captures the mafia/camora pretty well , as does "the last of the good guys" by John Carbone
The innocent is a relative of an enemy assassin. The mob boss had a relative (also an innocent) killed in the collateral damage of the enemy assassin's whacking someone else.
I don't know if someone actually suggested this already but hey, he's a mob, he might kill someone even for his satisfaction, maybe cause he's a psycho who likes to free his frustration on others only for pleasure.
