Actually, WebGL games would be a lot more secure from piracy, because they would be online, and you could easily stop 99% of the piracy by requiring a login for the game. It's basically like the Diablo 3 model, only better. Because Diablo 3 should be easier to crack and play on private servers (not sure if even that has happened yet).
Making an "online game" instead of a native "PC game" is the best way to stop most of the piracy.