I think something's going to happen that will expose Mysterio, or he exposes himself because he wants to take credit for it and turn it into a Mysterio villain plot (because that's what he always does) that Peter will have to deal with.
MJ will be lucky if Peter is the only person she has to explain herself to if it comes out she knew he was the director the entire time and didn't do anything about it. I mean, to a certain extent she's basically been his accomplice or partner-in-crime.