Okay, here's my thinking on this. Let's say X reveals that Dr. Wily is faking, and Mega Man and Dr. Light actually believe him. What then? Do they have Wily arrested? Would the third Megaman game just not happen? What about the rest of the Megaman games? What about Zero? If Dr. Wily never creates Zero, what happens to the Cataclysm? Without the Cataclysm and the Maverick Virus (essentially inside Zero), what happens to the future as X knows it? So, in other words, everything X knows could be forever altered by this single point in time, if only Dr. Wily is not allowed to continue with his evil plans.
Now, you might consider the eradication of an entire timeline just a tad evil. Granted, a different future might be a better place, but one of the dangers with messing around with timelines is that you can't predict how the timeline will change, and you could end up making things much worse. So, assuming the eradication of X's timeline is pretty evil, wouldn't this all mean that one of the most evil things Wily could ever do would be to stop faking his amnesia, since it would ultimately change the future, possibly for the worst?
Not to mention that if Dr. Wily isn't allowed to continue with his evil ways, Bass will never be created either, and since Bass is the one that started this whole mess, none of this would happen if Bass hadn't been created, resulting in a major paradox that could ultimately destroy the universe. That's pretty evil.