We can basically only speculate of what really happened. We don´t know for sure.
What we do know is that the Genovese Family was extremely fractured during the 1960s and early 1970s. Thanks to wiretaps, we know that the ruling troika of Catena, Miranda and Eboli grew a distrust for eachother and Eboli was caught on tape badmouthing especially Catena. There were even talks about hitting people. There were also talks about Genovese getting hit if he was to be released from prison.
Eboli was the only one still supporting Genovese and when Genovese passed, Eboli found himself on the outside looking in. He lost his face and was disgraced.
At the end of his time, I believe, he rubbed many people the wrong way and was killed for it.

The story about him losing money because of Louie Cirillo getting caught, is in my opinion just rumors on the street speculated at that time. I think someone in lawenforcement started the rumors because he wanted to connect the Cirillo bust with the murder of Eboli. People seems to want to feel important when providing answers, even if they are wrong. The story, however, stuck and apparently still circulates the internet today.

I very much doubt that Gambino would have allowed his money being invested into an operation he in 1963 forbade his members venturing in. It doesn´t make any sense. And besides, Louie Cirillo would certainly had paid with his life loosing Gambino´s and Eboli´s money. This never happened.