How does Prometheus know what Oliver's secret is? Simple, it's because Prometheus shares it too. he likes killing. The whole "avenge his father" thing is just an excuse, just like how Oliver becoming a vigilante was his excuse. It seems Prometheus recognizes that fact on some level, but that doesn't stop him trying to take the moral high ground (when he's actually worse than Oliver ever was).
Oliver's admission that he enjoys killing puts the previous four seasons under a new light. It explains why he didn't return home after Hong Kong, and why, even when there was a way to do things without killing, he always went for the lethal option. Ultimately, he didn't want to confront the possibility that the good man that everyone saw in him, from Laurel to Tommy, to Thea, and now Diggle and Felicity, had died on the shores of Lian Yu. It also explains why Ra's was adamant that Oliver be his successor — it wasn't just because of the prophecy, it was also because Ra's knew what Oliver was since the day the met, because that was who Ra's was. They both enjoyed killing, but not death, and registered it as wrong on some level, so they adopted a moral code to hold themselves back.
