I think the fandom puts more emphasis on Asimov's laws than the creators do. Technically, just shooting at Wily's contraptions in every single MM games puts a human at risk - Wily himself. Hell, every time the weakness is the glass of Wily's own cockpit! You are shooting *directly at Wily*. This puts him in harm's way because his contraptione exploding has the potential to harm the occupant inside. So ... MM actively violates Asimov's first rule in every single game.
In terms of Asimov's laws, a robot wouldn't be able to harm a human in order to help another human. It could use itself to physically shield one from the other, or restrain one perhapse, but not to harm one.
In terms of Megaman himself, I think the game shows the hesitation in MM. I don't think he would have done it, ultimately. After all, he wouldn't need to charge up to kill Wily. A few "pew pew pew"s to the head and Wily's toast, I'd say.