Everyone knows that the whole time it was actually Yui doing everything!
Nah, man. Everyone knows Silica was behind everything. Keep up, gramps.
Nah, mate. It was Sachi. Ain't nobody going to look for a 'dead' girl.
IDK, the whole thing about Kayaba being willing to go through with it was that it was literally his life's work, he'd spent his entire life from early childhood working towards realizing this fantasy. Not sure I buy Random Administrative Assistant/Code-monkey #3 saying, "Gee, your plan to condemn thousands of people to death for the sake of your power fantasy sure does sound swell!", never mind Kayaba actually bringing anyone else in on his plan.
Well, this is an AU where at least three canon characters have vague counterparts. I see your point, but the whole Anthropic Principle thing sort of necessitates someone with access to Kayaba's code started it off, if not Kayaba himself.