Nice post, however, I would disagree with your conclusion. The CEO is a negative character (I think the "most powerful person in the room" speech makes that clear). He is the head of Evil Corp. This pretty much the same, immoral, soulless mega corporation cliché we've seen a thousand times.
If the creators wanted to program us to prefer centralised currencies over Bitcoin, they wouldn't do it by having the villain of the show advocating it.
RE: Mr. Robot's ECoin v.s. Bitcoin