The difference between Wily and Manson is that the people who actually did the killings did so either a) under Manson's direct orders or b) under Manson's influence. On the other hand--wait I just thought of something: If the comic is anything to go by (since the Archie Comics Mega Man Arc "Blackout:The Curse of Ra Moon" is based on the events of Super Adventure Rockman), Wily did build device that enabled Ra Moon to spread his EMP all over the world. The only thing is; I am not sure if in the game, those helicopters crashed before or after Wily provided Ra Moon with Wily's EMP amplifying device.
I don't know anything about that specific incident, but there are many others where the robot masters caused widespread destruction at Wily's command (most notably MM5 and 7). It isn't shown on screen if anyone died in the attacks, though given that many buildings were destroyed it's highly likely. Those two incidents alone are instant terrorism charges.
And having looked up the plot for MM9, turning things around on Dr. Light probably wouldn't work either. Wily tried it and failed.
I don't know how valid an argument this is on this board, but if Keiji Inafune said (or implied) that no one died during Wily's schemes, then that is how it goes. He was employed with Capcom at the time that SAR was originally released. He was very upset with Super Adventure Rockman due to the fact that there were human deaths in the storyline, and he stated in an interview that he felt it was necessary to apologise to the fans for Super Adventure Rockman. He also said in the interview that if it were up to him, he would have made it so the pilots would have gotten away safely, but the game was too far along in production for Inafune-san to have any meaningful influence. That tells me that no one died during Wily's attacks on the world.
OBJECTION!
Or something....
The MunchKING is Back! And he is AWSOME!