I really don't know what is fact and what is spin, and I assume, most people don't (apart from the parties directly involved). Yes, there are a lot of questions, but that's inevitable when the details of the charges and evidence haven't been made public yet.
My gut feeling is that there may have been some "circumstantial" and perhaps "strongly suggestive" threads of "wrong-doing" that the NRL came across in their investigation... perhaps even a substantial amount of it painting a picture. Looking at all the pieces, it may well have seemed pretty clear to the average person that there was some shady stuff going on. However, they probably lacked real solid proof (in legal terms).
Then, with all the other political factors coming in, we ended up where we are now. It's only my hunch. I certainly hope the Penns fight it, and some clarity comes out; not just on what Manly may or may not have done, but shine a light on the shady practices in this area and perhaps lead to some reform.