I've made some conclusions which may be faulty, but I'll choose to believe in for now. I welcome all criticism and scrutiny on this matter. That being said, here's what I think.
The act of killing Dr A to prevent the damage he will cause fulfills the mission of preventing the damage he will cause. But killing might not be the optimal solution. The act of killing Dr A serves the purpose of incapacitating him thus preventing the damage. But what if it doesn't? What if Dr A wasn't the actual criminal? Or what if Dr A had more partners or had a cure for the drug/disease or the code for the nuke to disable it, etc. In this case, all the facts must be accounted for in order to justify the killing. And of course, it's usually impossible to have all the facts in any such case unless you or Mr B is directly involved in all such cases. This is point number one.
Point number two is that whatever judgement can be attributed to Dr A, the same judgement can't be directly attached to any other criminal as their situations will always be different. If Dr A is killed and no one else is hurt, that's good, but if Dr B is killed, the consequences might be different. Thus there can never be an answer that directly applies to all situations such as "yes, it's ok to kill criminals" or "no, you should never kill anyone." There are no absolutes for this situation and every action will have it's own consequences. Only with experience may one judge which is the lesser evil.
Point three is the matter of the options available for handling the situation. In an ideal world, something like an omnipotent God could have prevented someone like Dr A from ever existing, or even better, changed the facts in Dr A's life to make him become a good person. An All powerful king could have Dr A be captured and reformed to use his knowledge for the good of his kingdom. A superhero or an advanced military team might be able to kidnap or capture Dr A alive for further processing, and an incorruptible justice system could ensure Dr A never harms another person. And finally, A lone person with a gun, in the right place at the right time can only hope to shoot Dr A and hope all of his evils die with him. Ultimately it is certain that Dr A must be prevented from doing further harm.
With these points, I will conclude that killing Dr A should be a last resort option when all other options are unavailable, but it is a resort that must be taken to save the millions of live that would otherwise be lost. Should Citizen B be labeled evil for this action? No, not at all. Should he be known as a hero? Still no, as Dr A was not brought to justice and not made to pay his dues for lives he has taken. But that said, citizen B is definitely the savior of millions of lives, so he's not too bad of a person.
Now, If citizen B had the power and opportunity to kill Dr A But chose not to do so and let him kill millions of people, then he is at least half as bad if not more so than Dr A, and the blood of those people is similarly on his hands. It's never alright to let a killer go free to kill more innocent people, when you have the power to stop it.