It depends on your perspective. Some might view Dr. Manhattan as a villain because of the way his powers and choices impact the story and other characters. But others might see him as more of an anti-hero or a morally ambiguous figure.
It's a matter of debate. Some might argue there are other characters with equally or more powerful abilities. But Dr Manhattan's powers are indeed incredibly vast and might put him at the top for many.
Well, there have been multiple instances and different villains who could be considered as having killed Dr Strange in the comics. One such notable villain was Kaecilius in a particular storyline.